diff --git a/includes/data/software.yml b/includes/data/software.yml index ae3b50e6f..7ec216959 100644 --- a/includes/data/software.yml +++ b/includes/data/software.yml @@ -348,33 +348,39 @@ software_modules: versions: - {description: GNU Midnight Commander is a visual file manager., markedDefault: false, versionName: 4.8.29} - - categories: system, libs - defaultVersionName: 1.8.2 - description: Libgcrypt is a general purpose cryptographic library originally - based on code from GnuPG. - package: libgcrypt - url: https://www.gnupg.org/software/libgcrypt + - categories: system, compression + defaultVersionName: 1.5.2 + description: Zstandard, or zstd, is a fast lossless compression algorithm, targeting + real-time compression scenarios at zlib-level and better compression ratios. + package: zstd + url: https://github.com/facebook/zstd versions: - - {description: Libgcrypt is a general purpose cryptographic library originally - based on code from GnuPG., markedDefault: false, versionName: 1.8.2} - - categories: system, tools - defaultVersionName: 2.2.3 - description: Expat is a stream-oriented XML parser library written in C. - package: expat - url: http://libexpat.github.io + - {description: 'Zstandard, or zstd, is a fast lossless compression algorithm, + targeting real-time compression scenarios at zlib-level and better compression + ratios.', markedDefault: false, versionName: 1.5.2} + - categories: system, checkpointing + defaultVersionName: 2.6.0 + description: DMTCP (Distributed MultiThreaded Checkpointing) transparently checkpoints + a single-host or distributed computation in user-space -- with no modifications + to user code or to the O/S. + package: dmtcp + url: http://dmtcp.sourceforge.net/ versions: - - {description: Expat is a stream-oriented XML parser library written in C., - markedDefault: false, versionName: 2.2.3} - - categories: system, scm - defaultVersionName: 1.12.2 - description: Subversion is an open source version control system. - package: subversion - url: https://subversion.apache.org/ + - {description: DMTCP (Distributed MultiThreaded Checkpointing) transparently + checkpoints a single-host or distributed computation in user-space -- with + no modifications to user code or to the O/S., markedDefault: false, versionName: 2.6.0} + - categories: system, job management + defaultVersionName: 1.1.2 + description: DRMAA for Slurm Workload Manager (Slurm) is an implementation of + Open Grid Forum Distributed Resource Management Application API (DRMAA) version + 1 for submission and control of jobs to Slurm. + package: slurm-drmaa + url: https://github.com/natefoo/slurm-drmaa versions: - - {description: Subversion is an open source version control system., markedDefault: false, - versionName: 1.9.7} - - {description: Subversion is an open source version control system., markedDefault: false, - versionName: 1.12.2} + - {description: DRMAA for Slurm Workload Manager (Slurm) is an implementation + of Open Grid Forum Distributed Resource Management Application API (DRMAA) + version 1 for submission and control of jobs to Slurm., markedDefault: false, + versionName: 1.1.2} - categories: system, document management defaultVersionName: 2.7.3 description: Pandoc is a universal document converter. @@ -393,31 +399,16 @@ software_modules: - {description: 'Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.', markedDefault: false, versionName: 1.0.18} - - categories: system, file transfer - defaultVersionName: 0.11.1 - description: mpiFileUtils is a suite of MPI-based tools to manage large datasets, - which may vary from large directory trees to large files. - package: mpifileutils - url: https://github.com/hpc/mpifileutils + - categories: system, libs + defaultVersionName: 2.1.2 + description: FTGL is a free cross-platform Open Source C++ library that uses + Freetype2 to simplify rendering fonts in OpenGL applications. + package: ftgl + url: https://sourceforge.net/projects/ftgl/ versions: - - description: mpiFileUtils is a suite of MPI-based tools to manage large datasets, - which may vary from large directory trees to large files. - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: 0.10.1 - - description: mpiFileUtils is a suite of MPI-based tools to manage large datasets, - which may vary from large directory trees to large files. - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: '0.11' - - description: mpiFileUtils is a suite of MPI-based tools to manage large datasets, - which may vary from large directory trees to large files. - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: 0.11.1 + - {description: FTGL is a free cross-platform Open Source C++ library that uses + Freetype2 to simplify rendering fonts in OpenGL applications., markedDefault: false, + versionName: 2.1.2} - categories: system, file transfer defaultVersionName: 1.65.0 description: 'Rclone is a command line program to sync files and directories @@ -496,18 +487,16 @@ software_modules: - {description: FLTK (pronounced 'fulltick') is a cross-platform C++ GUI toolkit., markedDefault: false, versionName: 1.3.4} - categories: system, libs - defaultVersionName: '10.40' - description: The PCRE22 library is a set of functions that implement regular - expression pattern matching using the same syntax and semantics as Perl 5. - package: pcre2 - url: http://www.pcre.org/ + defaultVersionName: 0.9.1 + description: libxkbcommon is a keyboard keymap compiler and support library + which processes a reduced subset of keymaps as defined by the XKB (X Keyboard + Extension) specification. + package: libxkbcommon + url: https://github.com/xkbcommon/libxkbcommon versions: - - {description: The PCRE22 library is a set of functions that implement regular - expression pattern matching using the same syntax and semantics as Perl - 5., markedDefault: false, versionName: '10.35'} - - {description: The PCRE22 library is a set of functions that implement regular - expression pattern matching using the same syntax and semantics as Perl - 5., markedDefault: false, versionName: '10.40'} + - {description: libxkbcommon is a keyboard keymap compiler and support library + which processes a reduced subset of keymaps as defined by the XKB (X Keyboard + Extension) specification., markedDefault: false, versionName: 0.9.1} - categories: system, libs defaultVersionName: '1.27' description: Libgpg-error is a small library that originally defined common @@ -607,13 +596,6 @@ software_modules: properties: parallel: {mpi: 1} versionName: 5.6.1 - - description: The OSU MicroBenchmarks carry out a variety of message passing - performance tests using MPI. - markedDefault: false - properties: - arch: {gpu: 1} - parallel: {mpi: 1} - versionName: 5.6.3 - description: The OSU MicroBenchmarks carry out a variety of message passing performance tests using MPI. markedDefault: false @@ -957,17 +939,6 @@ software_modules: versions: - {description: 'A library for parsing, editing, and saving EXIF data.', markedDefault: false, versionName: 0.6.21} - - categories: system, scm - defaultVersionName: 2.49.2 - description: gh is GitHub on the command line. It brings pull requests, issues, - and other GitHub concepts to the terminal next to where you are already working - with git and your code. - package: gh - url: https://cli.github.com/ - versions: - - {description: 'gh is GitHub on the command line. It brings pull requests, - issues, and other GitHub concepts to the terminal next to where you are - already working with git and your code.', markedDefault: false, versionName: 2.49.2} - categories: system, database defaultVersionName: 10.2.11 description: MariaDB is a community-developed fork of the MySQL relational database @@ -981,6 +952,25 @@ software_modules: - {description: MariaDB is a community-developed fork of the MySQL relational database management system intended to remain free under the GNU GPL., help: 'https://www.sherlock.stanford.edu/docs/software/using/mariadb', markedDefault: true, versionName: 10.2.11} + - categories: system, scm + defaultVersionName: 2.49.2 + description: gh is GitHub on the command line. It brings pull requests, issues, + and other GitHub concepts to the terminal next to where you are already working + with git and your code. + package: gh + url: https://cli.github.com/ + versions: + - {description: 'gh is GitHub on the command line. It brings pull requests, + issues, and other GitHub concepts to the terminal next to where you are + already working with git and your code.', markedDefault: false, versionName: 2.49.2} + - categories: system, libs + defaultVersionName: 2.12.4 + description: Fontconfig is a library for configuring and customizing font access. + package: fontconfig + url: https://www.freedesktop.org/wiki/Software/fontconfig + versions: + - {description: Fontconfig is a library for configuring and customizing font + access., markedDefault: false, versionName: 2.12.4} - categories: system, database defaultVersionName: '14.5' description: PostgreSQL is a powerful, open source object-relational database @@ -1009,22 +999,19 @@ software_modules: public-domain, SQL database engine.', markedDefault: false, versionName: 3.37.2} - {description: 'SQLite is a self-contained, high-reliability, embedded, full-featured, public-domain, SQL database engine.', markedDefault: false, versionName: 3.44.2} - - categories: system, libs - defaultVersionName: 2.12.4 - description: Fontconfig is a library for configuring and customizing font access. - package: fontconfig - url: https://www.freedesktop.org/wiki/Software/fontconfig - versions: - - {description: Fontconfig is a library for configuring and customizing font - access., markedDefault: false, versionName: 2.12.4} - - categories: system, libs - defaultVersionName: 0.3.5 - description: C++ implementation of the Google logging module. - package: glog - url: https://github.com/google/glog + - categories: system, benchmark + defaultVersionName: 2.1.19_py39 + description: LinkTest is a communication API benchmarking tool that tests point-to-point + connections. + package: py-linktest + url: https://www.fz-juelich.de/en/ias/jsc/services/user-support/jsc-software-tools/linktest versions: - - {description: C++ implementation of the Google logging module., markedDefault: false, - versionName: 0.3.5} + - description: LinkTest is a communication API benchmarking tool that tests + point-to-point connections. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: 2.1.19_py39 - categories: system, libs defaultVersionName: 1.4.4 description: JSON-GLib is a library providing serialization and deserialization @@ -1036,16 +1023,6 @@ software_modules: - {description: JSON-GLib is a library providing serialization and deserialization support for the JavaScript Object Notation (JSON) format described by RFC 4627., markedDefault: false, versionName: 1.4.4} - - categories: system, libs - defaultVersionName: '59.1' - description: ICU is a set of C/C++ and Java libraries providing Unicode and - Globalization support for software applications. - package: icu - url: http://site.icu-project.org - versions: - - {description: ICU is a set of C/C++ and Java libraries providing Unicode and - Globalization support for software applications., markedDefault: false, - versionName: '59.1'} - categories: system, language defaultVersionName: 8.6.6 description: Tcl (Tool Command Language) is a dynamic programming language, @@ -1057,6 +1034,16 @@ software_modules: - {description: 'Tcl (Tool Command Language) is a dynamic programming language, suitable for web and desktop applications, networking, administration, testing. Tk is a graphical user interface toolkit.', markedDefault: false, versionName: 8.6.6} + - categories: system, libs + defaultVersionName: '59.1' + description: ICU is a set of C/C++ and Java libraries providing Unicode and + Globalization support for software applications. + package: icu + url: http://site.icu-project.org + versions: + - {description: ICU is a set of C/C++ and Java libraries providing Unicode and + Globalization support for software applications., markedDefault: false, + versionName: '59.1'} - categories: system, libs defaultVersionName: 2.9.91 description: GConf is a system for storing application preferences. @@ -1065,14 +1052,6 @@ software_modules: versions: - {description: GConf is a system for storing application preferences., markedDefault: false, versionName: 2.9.91} - - categories: system, file management - defaultVersionName: 0.8.0 - description: exa is a replacement for ls written in Rust. - package: exa - url: https://github.com/ogham/exa - versions: - - {description: exa is a replacement for ls written in Rust., markedDefault: false, - versionName: 0.8.0} - categories: system, libs defaultVersionName: 0.6.1 description: WebP is a modern image format that provides superior lossless and @@ -1082,6 +1061,14 @@ software_modules: versions: - {description: WebP is a modern image format that provides superior lossless and lossy compression for images on the web., markedDefault: false, versionName: 0.6.1} + - categories: system, file management + defaultVersionName: 0.8.0 + description: exa is a replacement for ls written in Rust. + package: exa + url: https://github.com/ogham/exa + versions: + - {description: exa is a replacement for ls written in Rust., markedDefault: false, + versionName: 0.8.0} - categories: system, libs defaultVersionName: 1.52.1 description: GObject introspection is a middleware layer between C libraries @@ -1091,19 +1078,26 @@ software_modules: versions: - {description: GObject introspection is a middleware layer between C libraries (using GObject) and language bindings., markedDefault: false, versionName: 1.52.1} - - categories: system, benchmark - defaultVersionName: 2.1.19_py39 - description: LinkTest is a communication API benchmarking tool that tests point-to-point - connections. - package: py-linktest - url: https://www.fz-juelich.de/en/ias/jsc/services/user-support/jsc-software-tools/linktest + - categories: system, libs + defaultVersionName: 2.36.8 + description: The GdkPixbuf library provides facilities for loading images in + a variety of file formats. + package: gdk-pixbuf + url: https://git.gnome.org/browse/gdk-pixbuf versions: - - description: LinkTest is a communication API benchmarking tool that tests - point-to-point connections. - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: 2.1.19_py39 + - {description: The GdkPixbuf library provides facilities for loading images + in a variety of file formats., markedDefault: false, versionName: 2.36.8} + - categories: system, libs + defaultVersionName: 1.6.1 + description: The Apache Portable Runtime is a supporting library for the Apache + web server. It provides a set of APIs that map to the underlying operating + system. + package: apr-util + url: https://apr.apache.org/ + versions: + - {description: The Apache Portable Runtime is a supporting library for the + Apache web server. It provides a set of APIs that map to the underlying + operating system., markedDefault: false, versionName: 1.6.1} - categories: system, file transfer defaultVersionName: 3.19.0_py39 description: A command line wrapper over the Globus SDK for Python. @@ -1156,33 +1150,30 @@ software_modules: - {description: The Portable Hardware Locality (hwloc) software package provides a portable abstraction of the hierarchical topology of modern architectures., markedDefault: false, versionName: 2.9.3} - - categories: system, libs - defaultVersionName: 1.6.1 - description: The Apache Portable Runtime is a supporting library for the Apache - web server. It provides a set of APIs that map to the underlying operating - system. - package: apr-util - url: https://apr.apache.org/ - versions: - - {description: The Apache Portable Runtime is a supporting library for the - Apache web server. It provides a set of APIs that map to the underlying - operating system., markedDefault: false, versionName: 1.6.1} - categories: system, compression - defaultVersionName: 1.8.0 - description: LZ4 is lossless compression algorithm. - package: lz4 - url: https://www.lz4.org - versions: - - {description: LZ4 is lossless compression algorithm., markedDefault: false, - versionName: 1.8.0} - - categories: system, libs - defaultVersionName: '1.0' - description: Implementation of a minimal subset of the PMI1 and PMI2 specifications. - package: minipmi - url: https://github.com/kraused/minipmi + defaultVersionName: 3.5.2 + description: The libarchive project develops a portable, efficient C library + that can read and write streaming archives in a variety of formats. + package: libarchive + url: https://www.libarchive.org/ versions: - - {description: Implementation of a minimal subset of the PMI1 and PMI2 specifications., - markedDefault: false, versionName: '1.0'} + - {description: 'The libarchive project develops a portable, efficient C library + that can read and write streaming archives in a variety of formats.', markedDefault: false, + versionName: 3.3.2} + - {description: 'The libarchive project develops a portable, efficient C library + that can read and write streaming archives in a variety of formats.', markedDefault: false, + versionName: 3.4.2} + - {description: 'The libarchive project develops a portable, efficient C library + that can read and write streaming archives in a variety of formats.', markedDefault: false, + versionName: 3.5.2} + - categories: system, compression + defaultVersionName: 1.8.0 + description: LZ4 is lossless compression algorithm. + package: lz4 + url: https://www.lz4.org + versions: + - {description: LZ4 is lossless compression algorithm., markedDefault: false, + versionName: 1.8.0} - categories: system, file management defaultVersionName: 2.8.0 description: rmlint finds space waste and other broken things on your filesystem @@ -1192,17 +1183,6 @@ software_modules: versions: - {description: rmlint finds space waste and other broken things on your filesystem and offers to remove it., markedDefault: false, versionName: 2.8.0} - - categories: system, libs - defaultVersionName: 1.7.7 - description: Scalable I/O library for parallel access to task-local files. - package: sionlib - url: https://www.fz-juelich.de/en/ias/jsc/services/user-support/jsc-software-tools/sionlib - versions: - - description: Scalable I/O library for parallel access to task-local files. - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: 1.7.7 - categories: system, libs defaultVersionName: 2.14.19 description: ORBit2 is a CORBA 2.4-compliant Object Request Broker (ORB) featuring @@ -1212,6 +1192,22 @@ software_modules: versions: - {description: 'ORBit2 is a CORBA 2.4-compliant Object Request Broker (ORB) featuring mature C, C++ and Python bindings.', markedDefault: false, versionName: 2.14.19} + - categories: system, tools + defaultVersionName: 1.3.26 + description: GraphicsMagick is the swiss army knife of image processing. + package: graphicsmagick + url: http://www.graphicsmagick.org/ + versions: + - {description: GraphicsMagick is the swiss army knife of image processing., + markedDefault: false, versionName: 1.3.26} + - categories: system, libs + defaultVersionName: 2.13.1 + description: C library for encoding, decoding and manipulating JSON data. + package: jansson + url: https://github.com/akheron/jansson + versions: + - {description: 'C library for encoding, decoding and manipulating JSON data.', + markedDefault: false, versionName: 2.13.1} - categories: system, libs defaultVersionName: 1.6.3 description: The Apache Portable Runtime is a supporting library for the Apache @@ -1241,15 +1237,6 @@ software_modules: - {description: 'GNU Libtool is a generic library support script that hides the complexity of using shared libraries behind a consistent, portable interface.', markedDefault: false, versionName: 2.4.7} - - categories: system, libs - defaultVersionName: 1.14.10 - description: Cairo is a 2D graphics library with support for multiple output - devices. - package: cairo - url: https://www.cairographics.org/ - versions: - - {description: Cairo is a 2D graphics library with support for multiple output - devices., markedDefault: false, versionName: 1.14.10} - categories: system, document processing defaultVersionName: 9.53.2 description: Ghostscript is an interpreter for the PostScript language and PDF @@ -1259,16 +1246,6 @@ software_modules: versions: - {description: Ghostscript is an interpreter for the PostScript language and PDF files., markedDefault: false, versionName: 9.53.2} - - categories: system, file transfer - defaultVersionName: 3.2.1_py39 - description: HTTPie is a command-line HTTP client designed for testing, debugging, - and generally interacting with APIs and HTTP servers. - package: py-httpie - url: https://httpie.io/ - versions: - - {description: 'HTTPie is a command-line HTTP client designed for testing, - debugging, and generally interacting with APIs and HTTP servers.', markedDefault: false, - versionName: 3.2.1_py39} - categories: system, libs defaultVersionName: 2.28.4 description: WebKitGTK is a full-featured port of the WebKit rendering engine, @@ -1281,6 +1258,16 @@ software_modules: suitable for projects requiring any kind of web integration, from hybrid HTML/CSS applications to full-fledged web browsers.', markedDefault: false, versionName: 2.28.4} + - categories: system, file transfer + defaultVersionName: 3.2.1_py39 + description: HTTPie is a command-line HTTP client designed for testing, debugging, + and generally interacting with APIs and HTTP servers. + package: py-httpie + url: https://httpie.io/ + versions: + - {description: 'HTTPie is a command-line HTTP client designed for testing, + debugging, and generally interacting with APIs and HTTP servers.', markedDefault: false, + versionName: 3.2.1_py39} - categories: system, libs defaultVersionName: 2.52.3 description: The GLib library provides core non-graphical functionality such @@ -1292,6 +1279,19 @@ software_modules: - {description: 'The GLib library provides core non-graphical functionality such as high level data types, Unicode manipulation, and an object and type system to C programs.', markedDefault: false, versionName: 2.52.3} + - categories: system, libs + defaultVersionName: '10.40' + description: The PCRE22 library is a set of functions that implement regular + expression pattern matching using the same syntax and semantics as Perl 5. + package: pcre2 + url: http://www.pcre.org/ + versions: + - {description: The PCRE22 library is a set of functions that implement regular + expression pattern matching using the same syntax and semantics as Perl + 5., markedDefault: false, versionName: '10.35'} + - {description: The PCRE22 library is a set of functions that implement regular + expression pattern matching using the same syntax and semantics as Perl + 5., markedDefault: false, versionName: '10.40'} - categories: system, resource monitoring defaultVersionName: 3.0.2 description: Nvtop stands for NVidia TOP, a (h)top like task monitor for NVIDIA @@ -1324,17 +1324,6 @@ software_modules: url: https://gitlab.freedesktop.org/xorg/lib/libpciaccess versions: - {description: Generic PCI access library., markedDefault: false, versionName: '0.16'} - - categories: system, libs - defaultVersionName: 0.9.1 - description: libxkbcommon is a keyboard keymap compiler and support library - which processes a reduced subset of keymaps as defined by the XKB (X Keyboard - Extension) specification. - package: libxkbcommon - url: https://github.com/xkbcommon/libxkbcommon - versions: - - {description: libxkbcommon is a keyboard keymap compiler and support library - which processes a reduced subset of keymaps as defined by the XKB (X Keyboard - Extension) specification., markedDefault: false, versionName: 0.9.1} - categories: system, compression defaultVersionName: '0.6' description: MPIBZIP2 is a parallel implementation of the bzip2 block-sorting @@ -1359,18 +1348,23 @@ software_modules: versions: - {description: libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors., markedDefault: false, versionName: 1.2.0} - - categories: system, job management - defaultVersionName: 1.1.2 - description: DRMAA for Slurm Workload Manager (Slurm) is an implementation of - Open Grid Forum Distributed Resource Management Application API (DRMAA) version - 1 for submission and control of jobs to Slurm. - package: slurm-drmaa - url: https://github.com/natefoo/slurm-drmaa + - categories: system, tools + defaultVersionName: 2.2.3 + description: Expat is a stream-oriented XML parser library written in C. + package: expat + url: http://libexpat.github.io versions: - - {description: DRMAA for Slurm Workload Manager (Slurm) is an implementation - of Open Grid Forum Distributed Resource Management Application API (DRMAA) - version 1 for submission and control of jobs to Slurm., markedDefault: false, - versionName: 1.1.2} + - {description: Expat is a stream-oriented XML parser library written in C., + markedDefault: false, versionName: 2.2.3} + - categories: system, libs + defaultVersionName: 1.12.0 + description: GStreamer is a library for constructing graphs of media-handling + components. + package: gstreamer + url: https://gstreamer.freedesktop.org/ + versions: + - {description: GStreamer is a library for constructing graphs of media-handling + components., markedDefault: false, versionName: 1.12.0} - categories: system, tools defaultVersionName: 7.0.7-2 description: ImageMagick is a free and open-source software suite for displaying, @@ -1381,15 +1375,16 @@ software_modules: - {description: 'ImageMagick is a free and open-source software suite for displaying, converting, and editing raster image and vector image files.', markedDefault: false, versionName: 7.0.7-2} - - categories: system, libs - defaultVersionName: 1.12.0 - description: GStreamer is a library for constructing graphs of media-handling - components. - package: gstreamer - url: https://gstreamer.freedesktop.org/ + - categories: system, scm + defaultVersionName: 1.12.2 + description: Subversion is an open source version control system. + package: subversion + url: https://subversion.apache.org/ versions: - - {description: GStreamer is a library for constructing graphs of media-handling - components., markedDefault: false, versionName: 1.12.0} + - {description: Subversion is an open source version control system., markedDefault: false, + versionName: 1.9.7} + - {description: Subversion is an open source version control system., markedDefault: false, + versionName: 1.12.2} - categories: system, compression defaultVersionName: '2.10' description: LZO is a portable lossless data compression library written in @@ -1417,16 +1412,17 @@ software_modules: versions: - {description: Libxml2 is a XML C parser and toolkit., markedDefault: false, versionName: 2.9.4} - - categories: system, compression - defaultVersionName: 5.2.3 - description: XZ Utils, the successor to LZMA Utils, is free general-purpose - data compression software with a high compression ratio. - package: xz - url: http://tukaani.org/xz/ + - categories: system, libs + defaultVersionName: 1.7.7 + description: Scalable I/O library for parallel access to task-local files. + package: sionlib + url: https://www.fz-juelich.de/en/ias/jsc/services/user-support/jsc-software-tools/sionlib versions: - - {description: 'XZ Utils, the successor to LZMA Utils, is free general-purpose - data compression software with a high compression ratio.', markedDefault: false, - versionName: 5.2.3} + - description: Scalable I/O library for parallel access to task-local files. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: 1.7.7 - categories: system, compiler defaultVersionName: 1.3.3 description: MRC is a resource compiler that can create self-contained applications, @@ -1437,16 +1433,31 @@ software_modules: - {description: 'MRC is a resource compiler that can create self-contained applications, by including all the required data inside executable files.', markedDefault: false, versionName: 1.3.3} - - categories: system, compression - defaultVersionName: 1.5.2 - description: Zstandard, or zstd, is a fast lossless compression algorithm, targeting - real-time compression scenarios at zlib-level and better compression ratios. - package: zstd - url: https://github.com/facebook/zstd + - categories: system, file transfer + defaultVersionName: 0.11.1 + description: mpiFileUtils is a suite of MPI-based tools to manage large datasets, + which may vary from large directory trees to large files. + package: mpifileutils + url: https://github.com/hpc/mpifileutils versions: - - {description: 'Zstandard, or zstd, is a fast lossless compression algorithm, - targeting real-time compression scenarios at zlib-level and better compression - ratios.', markedDefault: false, versionName: 1.5.2} + - description: mpiFileUtils is a suite of MPI-based tools to manage large datasets, + which may vary from large directory trees to large files. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: 0.10.1 + - description: mpiFileUtils is a suite of MPI-based tools to manage large datasets, + which may vary from large directory trees to large files. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: '0.11' + - description: mpiFileUtils is a suite of MPI-based tools to manage large datasets, + which may vary from large directory trees to large files. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: 0.11.1 - categories: system, benchmark defaultVersionName: '3.2' description: 'Heavy Peer To Peer: a MPI based benchmark for network diagnostic.' @@ -1459,15 +1470,13 @@ software_modules: parallel: {mpi: 1} versionName: '3.2' - categories: system, libs - defaultVersionName: 2.1.2 - description: FTGL is a free cross-platform Open Source C++ library that uses - Freetype2 to simplify rendering fonts in OpenGL applications. - package: ftgl - url: https://sourceforge.net/projects/ftgl/ + defaultVersionName: 1.0.12 + description: The Free Implementation of the Unicode Bidirectional Algorithm. + package: fribidi + url: https://github.com/fribidi/fribidi versions: - - {description: FTGL is a free cross-platform Open Source C++ library that uses - Freetype2 to simplify rendering fonts in OpenGL applications., markedDefault: false, - versionName: 2.1.2} + - {description: The Free Implementation of the Unicode Bidirectional Algorithm., + markedDefault: false, versionName: 1.0.12} - categories: system, libs defaultVersionName: 0.8.14 description: The libIDL package contains libraries for Interface Definition @@ -1478,14 +1487,6 @@ software_modules: - {description: The libIDL package contains libraries for Interface Definition Language files. This is a specification for defining portable interfaces., markedDefault: false, versionName: 0.8.14} - - categories: system, libs - defaultVersionName: 1.0.12 - description: The Free Implementation of the Unicode Bidirectional Algorithm. - package: fribidi - url: https://github.com/fribidi/fribidi - versions: - - {description: The Free Implementation of the Unicode Bidirectional Algorithm., - markedDefault: false, versionName: 1.0.12} - categories: system, libs defaultVersionName: 3.0.0 description: FreeGLUT is a free-software/open-source alternative to the OpenGL @@ -1495,6 +1496,14 @@ software_modules: versions: - {description: FreeGLUT is a free-software/open-source alternative to the OpenGL Utility Toolkit (GLUT) library., markedDefault: false, versionName: 3.0.0} + - categories: system, tools + defaultVersionName: 11.0.1 + description: ripgrep recursively searches directories for a regex pattern. + package: ripgrep + url: https://github.com/BurntSushi/ripgrep + versions: + - {description: ripgrep recursively searches directories for a regex pattern., + markedDefault: false, versionName: 11.0.1} - categories: system, libs defaultVersionName: 2.61.2 description: libsoup is an HTTP client/server library for GNOME. @@ -1522,14 +1531,6 @@ software_modules: versions: - {description: Data Version Control or DVC is an open-source tool for data science and machine learning projects., markedDefault: false, versionName: 0.91.1_py36} - - categories: system, tools - defaultVersionName: 11.0.1 - description: ripgrep recursively searches directories for a regex pattern. - package: ripgrep - url: https://github.com/BurntSushi/ripgrep - versions: - - {description: ripgrep recursively searches directories for a regex pattern., - markedDefault: false, versionName: 11.0.1} - categories: system, libs defaultVersionName: 2.24.0 description: ATK is the Accessibility Toolkit. It provides a set of generic @@ -1577,6 +1578,13 @@ software_modules: versions: - {description: 'talloc is a hierarchical, reference counted memory pool system with destructors.', markedDefault: false, versionName: 2.1.14} + - categories: system, libs + defaultVersionName: 1.0.3 + description: Portable uuid C library. + package: libuuid + url: https://sourceforge.net/projects/libuuid + versions: + - {description: Portable uuid C library., markedDefault: false, versionName: 1.0.3} - categories: system, libs defaultVersionName: 2.0.3 description: THE reference library for reading, displaying, writing and examining @@ -1596,29 +1604,6 @@ software_modules: versions: - {description: tdu estimates the disk space occupied by all files in a given path., markedDefault: false, versionName: '1.36'} - - categories: system, libs - defaultVersionName: 1.0.3 - description: Portable uuid C library. - package: libuuid - url: https://sourceforge.net/projects/libuuid - versions: - - {description: Portable uuid C library., markedDefault: false, versionName: 1.0.3} - - categories: system, compression - defaultVersionName: 1.2.11 - description: zlib is designed to be a free, general-purpose, legally unencumbered - -- that is, not covered by any patents -- lossless data-compression library - for use on virtually any computer hardware and operating system. - package: zlib - url: http://zlib.net - versions: - - {description: 'zlib is designed to be a free, general-purpose, legally unencumbered - -- that is, not covered by any patents -- lossless data-compression library - for use on virtually any computer hardware and operating system.', markedDefault: false, - versionName: 1.3.1} - - {description: 'zlib is designed to be a free, general-purpose, legally unencumbered - -- that is, not covered by any patents -- lossless data-compression library - for use on virtually any computer hardware and operating system.', markedDefault: true, - versionName: 1.2.11} - categories: system, libs defaultVersionName: 1.6.44 description: libpng is the official PNG reference library. It supports almost @@ -1636,6 +1621,32 @@ software_modules: - {description: 'libpng is the official PNG reference library. It supports almost all PNG features, is extensible, and has been extensively tested for over 20 years.', markedDefault: false, versionName: 1.6.44} + - categories: system, compression + defaultVersionName: 1.2.11 + description: zlib is designed to be a free, general-purpose, legally unencumbered + -- that is, not covered by any patents -- lossless data-compression library + for use on virtually any computer hardware and operating system. + package: zlib + url: http://zlib.net + versions: + - {description: 'zlib is designed to be a free, general-purpose, legally unencumbered + -- that is, not covered by any patents -- lossless data-compression library + for use on virtually any computer hardware and operating system.', markedDefault: false, + versionName: 1.3.1} + - {description: 'zlib is designed to be a free, general-purpose, legally unencumbered + -- that is, not covered by any patents -- lossless data-compression library + for use on virtually any computer hardware and operating system.', markedDefault: true, + versionName: 1.2.11} + - categories: system, cloud interface + defaultVersionName: 448.0.0 + description: Command-line interface for Google Cloud Platform products and services. + package: google-cloud-sdk + url: https://cloud.google.com/sdk + versions: + - {description: Command-line interface for Google Cloud Platform products and + services., markedDefault: false, versionName: 400.0.0} + - {description: Command-line interface for Google Cloud Platform products and + services., markedDefault: false, versionName: 448.0.0} - categories: system, document processing defaultVersionName: 0.47.0 description: Poppler is a PDF rendering library. @@ -1670,15 +1681,15 @@ software_modules: - {description: 'Secure, cross-platform Git credential storage with authentication to GitHub, Azure Repos, and other popular Git hosting services.', markedDefault: false, versionName: 2.0.696} - - categories: system, file management - defaultVersionName: 2.2.1 - description: FDUPES is a program for identifying or deleting duplicate files - residing within specified directories. - package: fdupes - url: https://github.com/adrianlopezroche/fdupes - versions: - - {description: FDUPES is a program for identifying or deleting duplicate files - residing within specified directories., markedDefault: false, versionName: 2.2.1} + - categories: system, tools + defaultVersionName: 0.5.16 + description: MUNGE (MUNGE Uid 'N' Gid Emporium) is an authentication service + for creating and validating user credentials. + package: munge + url: https://dun.github.io/munge/ + versions: + - {description: MUNGE (MUNGE Uid 'N' Gid Emporium) is an authentication service + for creating and validating user credentials., markedDefault: false, versionName: 0.5.16} - categories: system, libs defaultVersionName: 0.6.13 description: Libcroco is a standalone css2 parsing and manipulation library. @@ -1767,24 +1778,14 @@ software_modules: - {description: 'Symas LMDB is an extraordinarily fast, memory-efficient database we developed for the Symas OpenLDAP Project.', markedDefault: false, versionName: 0.9.21} - categories: system, libs - defaultVersionName: 2.36.8 - description: The GdkPixbuf library provides facilities for loading images in - a variety of file formats. - package: gdk-pixbuf - url: https://git.gnome.org/browse/gdk-pixbuf - versions: - - {description: The GdkPixbuf library provides facilities for loading images - in a variety of file formats., markedDefault: false, versionName: 2.36.8} - - categories: system, file transfer - defaultVersionName: 4.8.1 - description: LFTP is a sophisticated file transfer program supporting a number - of network protocols (ftp, http, sftp, fish, torrent). - package: lftp - url: https://lftp.yar.ru/ + defaultVersionName: 1.14.10 + description: Cairo is a 2D graphics library with support for multiple output + devices. + package: cairo + url: https://www.cairographics.org/ versions: - - {description: 'LFTP is a sophisticated file transfer program supporting a - number of network protocols (ftp, http, sftp, fish, torrent).', markedDefault: false, - versionName: 4.8.1} + - {description: Cairo is a 2D graphics library with support for multiple output + devices., markedDefault: false, versionName: 1.14.10} - categories: system, benchmark defaultVersionName: '29.4' description: mprime is used by GIMPS, a distributed computing project dedicated @@ -1806,6 +1807,16 @@ software_modules: - {description: 'The XCB util modules provides a number of libraries which sit on top of libxcb, the core X protocol library, and some of the extension libraries.', markedDefault: false, versionName: 0.1.5} + - categories: system, file transfer + defaultVersionName: 4.8.1 + description: LFTP is a sophisticated file transfer program supporting a number + of network protocols (ftp, http, sftp, fish, torrent). + package: lftp + url: https://lftp.yar.ru/ + versions: + - {description: 'LFTP is a sophisticated file transfer program supporting a + number of network protocols (ftp, http, sftp, fish, torrent).', markedDefault: false, + versionName: 4.8.1} - categories: system, libs defaultVersionName: 1.82.0 description: Leptonica is an open source library containing software that is @@ -1909,16 +1920,15 @@ software_modules: - {description: Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency., markedDefault: false, versionName: 2.45.1} - - categories: system, cloud interface - defaultVersionName: 448.0.0 - description: Command-line interface for Google Cloud Platform products and services. - package: google-cloud-sdk - url: https://cloud.google.com/sdk + - categories: system, file management + defaultVersionName: 2.2.1 + description: FDUPES is a program for identifying or deleting duplicate files + residing within specified directories. + package: fdupes + url: https://github.com/adrianlopezroche/fdupes versions: - - {description: Command-line interface for Google Cloud Platform products and - services., markedDefault: false, versionName: 400.0.0} - - {description: Command-line interface for Google Cloud Platform products and - services., markedDefault: false, versionName: 448.0.0} + - {description: FDUPES is a program for identifying or deleting duplicate files + residing within specified directories., markedDefault: false, versionName: 2.2.1} - categories: system, libs defaultVersionName: 1.40.10 description: Pango is a library for laying out and rendering of text, with an @@ -1938,15 +1948,6 @@ software_modules: - {description: Libxslt is the XSLT C library developed for the GNOME project. XSLT itself is a an XML language to define transformation for XML., markedDefault: false, versionName: 1.1.32} - - categories: system, cloud interface - defaultVersionName: 2.0.50 - description: This package provides a unified command line interface to Amazon - Web Services. - package: aws-cli - url: https://github.com/aws/aws-cli - versions: - - {description: This package provides a unified command line interface to Amazon - Web Services., markedDefault: false, versionName: 2.0.50} - categories: system, libs defaultVersionName: '3.3' description: Nettle is a cryptographic library that is designed to fit easily @@ -1956,22 +1957,6 @@ software_modules: versions: - {description: Nettle is a cryptographic library that is designed to fit easily in more or less any context., markedDefault: false, versionName: '3.3'} - - categories: system, tools - defaultVersionName: '2.21' - description: The non-arch keyboard configuration database for X Window. - package: xkeyboard-config - url: https://www.freedesktop.org/wiki/Software/XKeyboardConfig/ - versions: - - {description: The non-arch keyboard configuration database for X Window., - markedDefault: false, versionName: '2.21'} - - categories: system, libs - defaultVersionName: 5.1.0 - description: Tesseract is an open source text recognition (OCR) Engine. - package: tesseract - url: https://tesseract-ocr.github.io/ - versions: - - {description: Tesseract is an open source text recognition (OCR) Engine., - markedDefault: false, versionName: 5.1.0} - categories: system, tools defaultVersionName: 12.560.30_py312 description: Python bindings to the NVIDIA Management Library. @@ -1998,6 +1983,31 @@ software_modules: properties: arch: {gpu: 1} versionName: 12.560.30_py312 + - categories: system, tools + defaultVersionName: '2.21' + description: The non-arch keyboard configuration database for X Window. + package: xkeyboard-config + url: https://www.freedesktop.org/wiki/Software/XKeyboardConfig/ + versions: + - {description: The non-arch keyboard configuration database for X Window., + markedDefault: false, versionName: '2.21'} + - categories: system, libs + defaultVersionName: 5.1.0 + description: Tesseract is an open source text recognition (OCR) Engine. + package: tesseract + url: https://tesseract-ocr.github.io/ + versions: + - {description: Tesseract is an open source text recognition (OCR) Engine., + markedDefault: false, versionName: 5.1.0} + - categories: system, cloud interface + defaultVersionName: 2.0.50 + description: This package provides a unified command line interface to Amazon + Web Services. + package: aws-cli + url: https://github.com/aws/aws-cli + versions: + - {description: This package provides a unified command line interface to Amazon + Web Services., markedDefault: false, versionName: 2.0.50} - categories: system, file transfer defaultVersionName: 3.9.6 description: The IBM Aspera Command-Line Interface (the Aspera CLI) is a collection @@ -2021,25 +2031,15 @@ software_modules: family: qt, markedDefault: false, versionName: 4.2.0_py39} - {description: 'wxPython is the cross-platform GUI toolkit for the Python language,', family: qt, markedDefault: false, versionName: 4.2.1_py312} - - categories: system, tools - defaultVersionName: 1.3.26 - description: GraphicsMagick is the swiss army knife of image processing. - package: graphicsmagick - url: http://www.graphicsmagick.org/ - versions: - - {description: GraphicsMagick is the swiss army knife of image processing., - markedDefault: false, versionName: 1.3.26} - - categories: system, checkpointing - defaultVersionName: 2.6.0 - description: DMTCP (Distributed MultiThreaded Checkpointing) transparently checkpoints - a single-host or distributed computation in user-space -- with no modifications - to user code or to the O/S. - package: dmtcp - url: http://dmtcp.sourceforge.net/ + - categories: system, libs + defaultVersionName: 1.8.2 + description: Libgcrypt is a general purpose cryptographic library originally + based on code from GnuPG. + package: libgcrypt + url: https://www.gnupg.org/software/libgcrypt versions: - - {description: DMTCP (Distributed MultiThreaded Checkpointing) transparently - checkpoints a single-host or distributed computation in user-space -- with - no modifications to user code or to the O/S., markedDefault: false, versionName: 2.6.0} + - {description: Libgcrypt is a general purpose cryptographic library originally + based on code from GnuPG., markedDefault: false, versionName: 1.8.2} - categories: system, libs defaultVersionName: 2.3.3 description: The libseccomp library provides an easy to use, platform independent, @@ -2050,15 +2050,6 @@ software_modules: - {description: 'The libseccomp library provides an easy to use, platform independent, interface to the Linux Kernel''s syscall filtering mechanism..', markedDefault: false, versionName: 2.3.3} - - categories: system, libs - defaultVersionName: 3.0.7 - description: OpenSSL is a full-featured toolkit for general-purpose cryptography - and secure communication. - package: openssl - url: https://www.openssl.org/ - versions: - - {description: OpenSSL is a full-featured toolkit for general-purpose cryptography - and secure communication., markedDefault: false, versionName: 3.0.7} - categories: system, libs defaultVersionName: 4.0.8 description: libtiff provides support for the Tag Image File Format (TIFF), @@ -2072,6 +2063,25 @@ software_modules: a widely used format for storing image data.', markedDefault: false, versionName: 4.5.0} - {description: 'libtiff provides support for the Tag Image File Format (TIFF), a widely used format for storing image data.', markedDefault: true, versionName: 4.0.8} + - categories: system, libs + defaultVersionName: 3.0.7 + description: OpenSSL is a full-featured toolkit for general-purpose cryptography + and secure communication. + package: openssl + url: https://www.openssl.org/ + versions: + - {description: OpenSSL is a full-featured toolkit for general-purpose cryptography + and secure communication., markedDefault: false, versionName: 3.0.7} + - categories: system, compression + defaultVersionName: 5.2.3 + description: XZ Utils, the successor to LZMA Utils, is free general-purpose + data compression software with a high compression ratio. + package: xz + url: http://tukaani.org/xz/ + versions: + - {description: 'XZ Utils, the successor to LZMA Utils, is free general-purpose + data compression software with a high compression ratio.', markedDefault: false, + versionName: 5.2.3} - categories: system, tools defaultVersionName: 5.9.1 description: QT is a cross-platform application framework that is used for developing @@ -2189,13 +2199,13 @@ software_modules: Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.', markedDefault: false, versionName: 1.17.0} - categories: system, libs - defaultVersionName: 2.13.1 - description: C library for encoding, decoding and manipulating JSON data. - package: jansson - url: https://github.com/akheron/jansson + defaultVersionName: '1.0' + description: Implementation of a minimal subset of the PMI1 and PMI2 specifications. + package: minipmi + url: https://github.com/kraused/minipmi versions: - - {description: 'C library for encoding, decoding and manipulating JSON data.', - markedDefault: false, versionName: 2.13.1} + - {description: Implementation of a minimal subset of the PMI1 and PMI2 specifications., + markedDefault: false, versionName: '1.0'} - categories: system, document processing defaultVersionName: 1.23.0 description: groff (GNU roff) is a typesetting system that reads plain text @@ -2225,22 +2235,14 @@ software_modules: - {description: dua (-> Disk Usage Analyzer) is a tool to conveniently learn about the usage of disk space of a given directory., markedDefault: false, versionName: 2.20.1} - - categories: system, compression - defaultVersionName: 3.5.2 - description: The libarchive project develops a portable, efficient C library - that can read and write streaming archives in a variety of formats. - package: libarchive - url: https://www.libarchive.org/ + - categories: system, resource monitoring + defaultVersionName: 1.8.5 + description: Remora is a tool to monitor runtime resource utilization. + package: remora + url: https://github.com/TACC/remora versions: - - {description: 'The libarchive project develops a portable, efficient C library - that can read and write streaming archives in a variety of formats.', markedDefault: false, - versionName: 3.3.2} - - {description: 'The libarchive project develops a portable, efficient C library - that can read and write streaming archives in a variety of formats.', markedDefault: false, - versionName: 3.4.2} - - {description: 'The libarchive project develops a portable, efficient C library - that can read and write streaming archives in a variety of formats.', markedDefault: false, - versionName: 3.5.2} + - {description: Remora is a tool to monitor runtime resource utilization., markedDefault: false, + versionName: 1.8.5} - categories: system, libs defaultVersionName: 3.32.2_py36 description: PyGObject is a Python package which provides bindings for GObject @@ -2260,14 +2262,6 @@ software_modules: versions: - {description: 'A parallel implementation of gzip for modern multi-processor, multi-core machines.', markedDefault: false, versionName: '2.4'} - - categories: system, tools - defaultVersionName: '20200731' - description: Tools for working with Chromium development. - package: depot_tools - url: https://chromium.googlesource.com/chromium/tools/depot_tools.git - versions: - - {description: Tools for working with Chromium development., markedDefault: false, - versionName: '20200731'} - categories: system, tools defaultVersionName: 0.10.0_py39 description: matlab-proxy is a Python package which enables you to launch MATLAB @@ -2279,14 +2273,22 @@ software_modules: MATLAB and access it from a web browser., markedDefault: false, versionName: 0.9.1_py39} - {description: matlab-proxy is a Python package which enables you to launch MATLAB and access it from a web browser., markedDefault: false, versionName: 0.10.0_py39} - - categories: system, resource monitoring - defaultVersionName: 1.8.5 - description: Remora is a tool to monitor runtime resource utilization. - package: remora - url: https://github.com/TACC/remora - versions: - - {description: Remora is a tool to monitor runtime resource utilization., markedDefault: false, - versionName: 1.8.5} + - categories: system, tools + defaultVersionName: '20200731' + description: Tools for working with Chromium development. + package: depot_tools + url: https://chromium.googlesource.com/chromium/tools/depot_tools.git + versions: + - {description: Tools for working with Chromium development., markedDefault: false, + versionName: '20200731'} + - categories: system, libs + defaultVersionName: 0.3.5 + description: C++ implementation of the Google logging module. + package: glog + url: https://github.com/google/glog + versions: + - {description: C++ implementation of the Google logging module., markedDefault: false, + versionName: 0.3.5} - categories: system, testing defaultVersionName: 7.1.3_py39 description: 'pytest is a full-featured Python testing framework ' @@ -4558,24 +4560,17 @@ software_modules: libraries for using data in the INSDC Sequence Read Archives., markedDefault: false, versionName: 3.0.7} - categories: biology, genomics - defaultVersionName: '202112.01' - description: Sentieon Genomics software is a set of software tools that perform - analysis of genomic data obtained from DNA sequencing. - package: sentieon - url: https://www.sentieon.com/ - versions: - - description: Sentieon Genomics software is a set of software tools that perform - analysis of genomic data obtained from DNA sequencing. - markedDefault: false - properties: - license: {restricted: 1} - versionName: '201808.01' - - description: Sentieon Genomics software is a set of software tools that perform - analysis of genomic data obtained from DNA sequencing. - markedDefault: false - properties: - license: {restricted: 1} - versionName: '202112.01' + defaultVersionName: 2.0.0 + description: The Bases2Fastq Software demultiplexess sequencing data from Element + instruments and converts base calls into FASTQ files for secondary analysis + with the FASTQ-compatible software of your choice. + package: bases2fastq + url: https://docs.elembio.io/docs/bases2fastq + versions: + - {description: The Bases2Fastq Software demultiplexess sequencing data from + Element instruments and converts base calls into FASTQ files for secondary + analysis with the FASTQ-compatible software of your choice., markedDefault: false, + versionName: 2.0.0} - categories: biology, pathology defaultVersionName: 1.1.1_py27 description: OpenSlide Python is a Python interface to the OpenSlide library. @@ -4779,17 +4774,21 @@ software_modules: the DICOM format to the NIfTI format., markedDefault: false, versionName: 1.0.20171215} - {description: dcm2niix is a program esigned to convert neuroimaging data from the DICOM format to the NIfTI format., markedDefault: false, versionName: 1.0.20211006} - - categories: biology, genomics - defaultVersionName: 0.98.5 - description: GEMMA is a software toolkit for fast application of linear mixed - models (LMMs) and related models to genome-wide association studies (GWAS) - and other large-scale data sets. - package: gemma - url: https://github.com/genetics-statistics/GEMMA + - categories: biology, computational biology + defaultVersionName: 1.84_py312 + description: Biopython is a set of freely available tools for biological computation + written in Python. + package: py-biopython + url: http://biopython.org versions: - - {description: GEMMA is a software toolkit for fast application of linear mixed - models (LMMs) and related models to genome-wide association studies (GWAS) - and other large-scale data sets., markedDefault: false, versionName: 0.98.5} + - {description: Biopython is a set of freely available tools for biological + computation written in Python., markedDefault: false, versionName: 1.70_py27} + - {description: Biopython is a set of freely available tools for biological + computation written in Python., markedDefault: false, versionName: 1.79_py36} + - {description: Biopython is a set of freely available tools for biological + computation written in Python., markedDefault: false, versionName: 1.79_py39} + - {description: Biopython is a set of freely available tools for biological + computation written in Python., markedDefault: false, versionName: 1.84_py312} - categories: biology, genomics defaultVersionName: 1.3.3 description: RSEM is a software package for estimating gene and isoform expression @@ -4911,15 +4910,16 @@ software_modules: - {description: 'HiC-Pro: An optimized and flexible pipeline for Hi-C data processing.', markedDefault: false, versionName: 2.10.0} - categories: biology, genomics - defaultVersionName: 0.38.1 - description: breseq is a computational pipeline for finding mutations relative - to a reference sequence in short-read DNA resequencing data. - package: breseq - url: http://barricklab.org/breseq + defaultVersionName: 0.98.5 + description: GEMMA is a software toolkit for fast application of linear mixed + models (LMMs) and related models to genome-wide association studies (GWAS) + and other large-scale data sets. + package: gemma + url: https://github.com/genetics-statistics/GEMMA versions: - - {description: breseq is a computational pipeline for finding mutations relative - to a reference sequence in short-read DNA resequencing data., markedDefault: false, - versionName: 0.38.1} + - {description: GEMMA is a software toolkit for fast application of linear mixed + models (LMMs) and related models to genome-wide association studies (GWAS) + and other large-scale data sets., markedDefault: false, versionName: 0.98.5} - categories: biology, cryo-em defaultVersionName: 4.11.5 description: IMOD is a set of image processing, modeling and display programs @@ -4943,53 +4943,25 @@ software_modules: arch: {gpu: 1} versionName: 4.11.5 - categories: biology, genomics - defaultVersionName: 2.3.4.1 - description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning - sequencing reads to long reference sequences. - package: bowtie2 - url: http://bowtie-bio.sourceforge.net/bowtie2 - versions: - - {description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning - sequencing reads to long reference sequences., markedDefault: false, versionName: 2.3.4.1} - - categories: biology, genomics - defaultVersionName: '1.16' - description: BCFtools is a program for variant calling and manipulating files - in the Variant Call Format (VCF) and its binary counterpart BCF. - package: bcftools - url: https://github.com/samtools/bcftools - versions: - - {description: BCFtools is a program for variant calling and manipulating files - in the Variant Call Format (VCF) and its binary counterpart BCF., markedDefault: false, - versionName: '1.6'} - - {description: BCFtools is a program for variant calling and manipulating files - in the Variant Call Format (VCF) and its binary counterpart BCF., markedDefault: false, - versionName: '1.8'} - - {description: BCFtools is a program for variant calling and manipulating files - in the Variant Call Format (VCF) and its binary counterpart BCF., markedDefault: false, - versionName: '1.16'} - - categories: biology, genomics - defaultVersionName: 0.11.8 - description: FastQC aims to provide a simple way to do some quality control - checks on raw sequence data coming from high throughput sequencing pipelines. - package: fastqc - url: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ + defaultVersionName: 0.38.1 + description: breseq is a computational pipeline for finding mutations relative + to a reference sequence in short-read DNA resequencing data. + package: breseq + url: http://barricklab.org/breseq versions: - - {description: FastQC aims to provide a simple way to do some quality control - checks on raw sequence data coming from high throughput sequencing pipelines., - markedDefault: false, versionName: 0.11.8} + - {description: breseq is a computational pipeline for finding mutations relative + to a reference sequence in short-read DNA resequencing data., markedDefault: false, + versionName: 0.38.1} - categories: biology, genomics - defaultVersionName: 0.7.3 - description: Dorado is a high-performance, easy-to-use, open source basecaller - for Oxford Nanopore reads. - package: dorado - url: https://github.com/nanoporetech/dorado + defaultVersionName: 1.1.3_py27 + description: Fit-Hi-C is a tool for assigning statistical confidence estimates + to chromosomal contact maps produced by genome architecture assays. + package: py-fithic + url: https://github.com/ay-lab/fithic versions: - - {description: 'Dorado is a high-performance, easy-to-use, open source basecaller - for Oxford Nanopore reads.', markedDefault: false, versionName: 0.3.4} - - {description: 'Dorado is a high-performance, easy-to-use, open source basecaller - for Oxford Nanopore reads.', markedDefault: false, versionName: 0.5.3} - - {description: 'Dorado is a high-performance, easy-to-use, open source basecaller - for Oxford Nanopore reads.', markedDefault: false, versionName: 0.7.3} + - {description: Fit-Hi-C is a tool for assigning statistical confidence estimates + to chromosomal contact maps produced by genome architecture assays., markedDefault: false, + versionName: 1.1.3_py27} - categories: biology, genomics defaultVersionName: 0.44.0 description: kallisto is a program for quantifying abundances of transcripts @@ -5006,6 +4978,43 @@ software_modules: - {description: kallisto is a program for quantifying abundances of transcripts from RNA-Seq data using high-throughput sequencing reads., markedDefault: true, versionName: 0.44.0} + - categories: biology, genomics + defaultVersionName: 3.3.1_py36 + description: Tools to process and analyze deep sequencing data. + package: py-deeptools + url: https://github.com/deeptools/deepTools/ + versions: + - {description: Tools to process and analyze deep sequencing data., markedDefault: false, + versionName: 3.3.1_py36} + - categories: biology, genomics + defaultVersionName: 0.11.8 + description: FastQC aims to provide a simple way to do some quality control + checks on raw sequence data coming from high throughput sequencing pipelines. + package: fastqc + url: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ + versions: + - {description: FastQC aims to provide a simple way to do some quality control + checks on raw sequence data coming from high throughput sequencing pipelines., + markedDefault: false, versionName: 0.11.8} + - categories: biology, genomics + defaultVersionName: 2.2.3_py39 + description: A software package for animal pose estimation. + package: py-deeplabcut + url: http://deeplabcut.org + versions: + - description: A software package for animal pose estimation. + markedDefault: false + properties: + arch: {gpu: 1} + versionName: 2.2.3_py39 + - categories: biology, genomics + defaultVersionName: 3.0.7 + description: NCBI VDB is the database engine used by NCBI SRA tools. + package: ncbi-vdb + url: https://github.com/ncbi/ncbi-vdb + versions: + - {description: NCBI VDB is the database engine used by NCBI SRA tools., markedDefault: false, + versionName: 3.0.7} - categories: biology, genomics defaultVersionName: 2.4.40 description: BEDOPS is an open-source command-line toolkit that performs highly @@ -5074,16 +5083,21 @@ software_modules: diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses.', markedDefault: false, versionName: 3.0.3} - categories: biology, genomics - defaultVersionName: 2.30.0 - description: The bedtools utilities are a swiss-army knife of tools for a wide-range - of genomics analysis tasks. - package: bedtools - url: https://bedtools.readthedocs.io + defaultVersionName: '1.16' + description: C library for high-throughput sequencing data formats. + package: htslib + url: https://github.com/samtools/htslib versions: - - {description: The bedtools utilities are a swiss-army knife of tools for a - wide-range of genomics analysis tasks., markedDefault: false, versionName: 2.27.1} - - {description: The bedtools utilities are a swiss-army knife of tools for a - wide-range of genomics analysis tasks., markedDefault: false, versionName: 2.30.0} + - {description: C library for high-throughput sequencing data formats., markedDefault: false, + versionName: '1.6'} + - {description: C library for high-throughput sequencing data formats., markedDefault: false, + versionName: '1.8'} + - {description: C library for high-throughput sequencing data formats., markedDefault: false, + versionName: 1.10.2} + - {description: C library for high-throughput sequencing data formats., markedDefault: false, + versionName: '1.14'} + - {description: C library for high-throughput sequencing data formats., markedDefault: false, + versionName: '1.16'} - categories: biology, neurology defaultVersionName: 7.4.1 description: An open source software suite for processing and analyzing (human) @@ -5102,29 +5116,24 @@ software_modules: - {description: An open source software suite for processing and analyzing (human) brain MRI images., markedDefault: false, versionName: 7.4.1} - categories: biology, genomics - defaultVersionName: 3.0.7 - description: NCBI VDB is the database engine used by NCBI SRA tools. - package: ncbi-vdb - url: https://github.com/ncbi/ncbi-vdb + defaultVersionName: 2.5.1 + description: BamTools is a project that provides both a C++ API and a command-line + toolkit for reading, writing, and manipulating BAM (genome alignment) files. + package: bamtools + url: https://github.com/pezmaster31/bamtools versions: - - {description: NCBI VDB is the database engine used by NCBI SRA tools., markedDefault: false, - versionName: 3.0.7} - - categories: biology, genomics - defaultVersionName: '1.16' - description: C library for high-throughput sequencing data formats. - package: htslib - url: https://github.com/samtools/htslib + - {description: 'BamTools is a project that provides both a C++ API and a command-line + toolkit for reading, writing, and manipulating BAM (genome alignment) files.', + markedDefault: false, versionName: 2.5.1} + - categories: biology, population genetics + defaultVersionName: 0.6.1_py36 + description: Admixfrog is a HMM to infer ancestry frogments (fragments) from + low-coverage, contaminated data. + package: py-admixfrog + url: https://github.com/BenjaminPeter/admixfrog versions: - - {description: C library for high-throughput sequencing data formats., markedDefault: false, - versionName: '1.6'} - - {description: C library for high-throughput sequencing data formats., markedDefault: false, - versionName: '1.8'} - - {description: C library for high-throughput sequencing data formats., markedDefault: false, - versionName: 1.10.2} - - {description: C library for high-throughput sequencing data formats., markedDefault: false, - versionName: '1.14'} - - {description: C library for high-throughput sequencing data formats., markedDefault: false, - versionName: '1.16'} + - {description: 'Admixfrog is a HMM to infer ancestry frogments (fragments) + from low-coverage, contaminated data.', markedDefault: false, versionName: 0.6.1_py36} - categories: biology, neurology defaultVersionName: 5.0.10 description: FSL is a comprehensive library of analysis tools for FMRI, MRI @@ -5144,27 +5153,26 @@ software_modules: properties: arch: {gpu: 1} versionName: 5.0.10 - - categories: biology, neurology - defaultVersionName: 0.7.00 - description: BART is a toolbox for Computational Magnetic Resonance Imaging. - package: bart - url: https://mrirecon.github.io/bart/ + - categories: biology, genomics + defaultVersionName: 2.30.0 + description: The bedtools utilities are a swiss-army knife of tools for a wide-range + of genomics analysis tasks. + package: bedtools + url: https://bedtools.readthedocs.io versions: - - description: BART is a toolbox for Computational Magnetic Resonance Imaging. - markedDefault: false - properties: - arch: {gpu: 1} - versionName: 0.7.00 + - {description: The bedtools utilities are a swiss-army knife of tools for a + wide-range of genomics analysis tasks., markedDefault: false, versionName: 2.27.1} + - {description: The bedtools utilities are a swiss-army knife of tools for a + wide-range of genomics analysis tasks., markedDefault: false, versionName: 2.30.0} - categories: biology, genomics - defaultVersionName: 2.5.1 - description: BamTools is a project that provides both a C++ API and a command-line - toolkit for reading, writing, and manipulating BAM (genome alignment) files. - package: bamtools - url: https://github.com/pezmaster31/bamtools + defaultVersionName: 0.0.14 + description: The FASTX-Toolkit is a collection of command line tools for Short-Reads + FASTA/FASTQ files preprocessing. + package: fastx_toolkit + url: http://hannonlab.cshl.edu/fastx_toolkit/ versions: - - {description: 'BamTools is a project that provides both a C++ API and a command-line - toolkit for reading, writing, and manipulating BAM (genome alignment) files.', - markedDefault: false, versionName: 2.5.1} + - {description: The FASTX-Toolkit is a collection of command line tools for + Short-Reads FASTA/FASTQ files preprocessing., markedDefault: false, versionName: 0.0.14} - categories: biology, genomics defaultVersionName: 1.2.2 description: Bowtie is an ultrafast, memory-efficient short read aligner. @@ -5231,23 +5239,21 @@ software_modules: - {description: FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms., markedDefault: false, versionName: 1.2.0} - categories: biology, genomics - defaultVersionName: 0.0.14 - description: The FASTX-Toolkit is a collection of command line tools for Short-Reads - FASTA/FASTQ files preprocessing. - package: fastx_toolkit - url: http://hannonlab.cshl.edu/fastx_toolkit/ - versions: - - {description: The FASTX-Toolkit is a collection of command line tools for - Short-Reads FASTA/FASTQ files preprocessing., markedDefault: false, versionName: 0.0.14} - - categories: biology, population genetics - defaultVersionName: 0.6.1_py36 - description: Admixfrog is a HMM to infer ancestry frogments (fragments) from - low-coverage, contaminated data. - package: py-admixfrog - url: https://github.com/BenjaminPeter/admixfrog + defaultVersionName: 0.4.17_py36 + description: A visualization framework for CRISPR/Cas9 knockout screens, analyzed + with MAGeCK. + package: py-vispr + url: https://bitbucket.org/liulab/vispr versions: - - {description: 'Admixfrog is a HMM to infer ancestry frogments (fragments) - from low-coverage, contaminated data.', markedDefault: false, versionName: 0.6.1_py36} + - {description: 'A visualization framework for CRISPR/Cas9 knockout screens, + analyzed with MAGeCK.', markedDefault: false, versionName: 0.4.17_py36} + - categories: biology, computational biology + defaultVersionName: .1.0.0_py312 + description: Biopython is a set of freely available tools for biological computation + written in Python. + package: py-scenicplus + url: http://biopython.org + versions: [] - categories: biology, genomics defaultVersionName: 2.0.1_py39 description: HTSeq is a Python library to facilitate processing and analysis @@ -5277,14 +5283,21 @@ software_modules: - {description: 'OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics.', markedDefault: false, versionName: 2.5.4_py39} - categories: biology, genomics - defaultVersionName: 0.4.17_py36 - description: A visualization framework for CRISPR/Cas9 knockout screens, analyzed - with MAGeCK. - package: py-vispr - url: https://bitbucket.org/liulab/vispr + defaultVersionName: 4.6.0.0 + description: GATK (Genome Analysis Toolkit) offers a wide variety of tools with + a primary focus on variant discovery and genotyping. + package: gatk + url: https://software.broadinstitute.org/gatk/ versions: - - {description: 'A visualization framework for CRISPR/Cas9 knockout screens, - analyzed with MAGeCK.', markedDefault: false, versionName: 0.4.17_py36} + - {description: GATK (Genome Analysis Toolkit) offers a wide variety of tools + with a primary focus on variant discovery and genotyping., markedDefault: false, + versionName: 4.1.0.0} + - {description: GATK (Genome Analysis Toolkit) offers a wide variety of tools + with a primary focus on variant discovery and genotyping., markedDefault: false, + versionName: 4.1.4.1} + - {description: GATK (Genome Analysis Toolkit) offers a wide variety of tools + with a primary focus on variant discovery and genotyping., markedDefault: false, + versionName: 4.6.0.0} - categories: biology, genomics defaultVersionName: 2.1.0 description: HISAT2 is a fast and sensitive alignment program for mapping next-generation @@ -5297,15 +5310,6 @@ software_modules: next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome)., markedDefault: false, versionName: 2.1.0} - - categories: biology, genomics - defaultVersionName: 2.1.0 - description: Cell Ranger ATAC is a set of analysis pipelines that process Chromium - Single Cell ATAC data. - package: cellranger-atac - url: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac - versions: - - {description: Cell Ranger ATAC is a set of analysis pipelines that process - Chromium Single Cell ATAC data., markedDefault: false, versionName: 2.1.0} - categories: biology, genomics defaultVersionName: 0.9.0_py39 description: Pybedtools wraps and extends BEDTools and offers feature-level @@ -5318,23 +5322,16 @@ software_modules: - {description: Pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python., markedDefault: false, versionName: 0.8.2_py36} - {description: Pybedtools wraps and extends BEDTools and offers feature-level - manipulations from within Python., markedDefault: false, versionName: 0.9.0_py39} - - categories: biology, genomics - defaultVersionName: 4.6.0.0 - description: GATK (Genome Analysis Toolkit) offers a wide variety of tools with - a primary focus on variant discovery and genotyping. - package: gatk - url: https://software.broadinstitute.org/gatk/ - versions: - - {description: GATK (Genome Analysis Toolkit) offers a wide variety of tools - with a primary focus on variant discovery and genotyping., markedDefault: false, - versionName: 4.1.0.0} - - {description: GATK (Genome Analysis Toolkit) offers a wide variety of tools - with a primary focus on variant discovery and genotyping., markedDefault: false, - versionName: 4.1.4.1} - - {description: GATK (Genome Analysis Toolkit) offers a wide variety of tools - with a primary focus on variant discovery and genotyping., markedDefault: false, - versionName: 4.6.0.0} + manipulations from within Python., markedDefault: false, versionName: 0.9.0_py39} + - categories: biology, genomics + defaultVersionName: 2.1.0 + description: Cell Ranger ATAC is a set of analysis pipelines that process Chromium + Single Cell ATAC data. + package: cellranger-atac + url: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac + versions: + - {description: Cell Ranger ATAC is a set of analysis pipelines that process + Chromium Single Cell ATAC data., markedDefault: false, versionName: 2.1.0} - categories: biology, genomics defaultVersionName: 0.8.13_py39 description: Tools for manipulating biological data, particularly multiple sequence @@ -5356,15 +5353,6 @@ software_modules: - {description: Nextflow is a bioinformatics workflow manager that enables the development of portable and reproducible workflows., markedDefault: false, versionName: 23.04.3} - - categories: biology, genomics - defaultVersionName: 2.5.1 - description: A C code library and several stand-alone programs for the prediction - and comparison of RNA secondary structures. - package: viennarna - url: https://github.com/ViennaRNA/ViennaRNA - versions: - - {description: A C code library and several stand-alone programs for the prediction - and comparison of RNA secondary structures., markedDefault: false, versionName: 2.5.1} - categories: biology, molecular biology defaultVersionName: 3.0.0 description: Library to work with mmCIF and PDB files. @@ -5373,39 +5361,25 @@ software_modules: versions: - {description: Library to work with mmCIF and PDB files., markedDefault: false, versionName: 3.0.0} - - categories: biology, computational biology - defaultVersionName: '3.14' - description: Rosetta is the premier software suite for modeling macromolecular - structures. As a flexible, multi-purpose application, it includes tools for - structure prediction, design, and remodeling of proteins and nucleic acids. - package: rosetta - url: https://www.rosettacommons.org + - categories: biology, genomics + defaultVersionName: 2.5.1 + description: A C code library and several stand-alone programs for the prediction + and comparison of RNA secondary structures. + package: viennarna + url: https://github.com/ViennaRNA/ViennaRNA versions: - - description: Rosetta is the premier software suite for modeling macromolecular - structures. As a flexible, multi-purpose application, it includes tools - for structure prediction, design, and remodeling of proteins and nucleic - acids. - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: '3.8' - - description: Rosetta is the premier software suite for modeling macromolecular - structures. As a flexible, multi-purpose application, it includes tools - for structure prediction, design, and remodeling of proteins and nucleic - acids. - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: '3.14' - - categories: biology, radiology - defaultVersionName: '4.2' - description: The NBIA Data Retriever is an application to download radiology - images from the TCIA Radiology Portal. - package: nbia-data-retriever - url: https://wiki.cancerimagingarchive.net/display/NBIA/Current+NBIA+Data+Retriever+Help + - {description: A C code library and several stand-alone programs for the prediction + and comparison of RNA secondary structures., markedDefault: false, versionName: 2.5.1} + - categories: biology, genomics + defaultVersionName: 2.13.1 + description: Trinity RNA-Seq de novo transcriptome assembly. + package: trinity + url: https://github.com/trinityrnaseq/trinityrnaseq versions: - - {description: The NBIA Data Retriever is an application to download radiology - images from the TCIA Radiology Portal., markedDefault: false, versionName: '4.2'} + - {description: Trinity RNA-Seq de novo transcriptome assembly., markedDefault: false, + versionName: 2.8.4} + - {description: Trinity RNA-Seq de novo transcriptome assembly., markedDefault: false, + versionName: 2.13.1} - categories: biology, cryo-em defaultVersionName: 0.2.5_py39 description: A pipeline for particle detection in cryo-electron microscopy images @@ -5427,6 +5401,25 @@ software_modules: properties: arch: {gpu: 1} versionName: 0.2.5_py39 + - categories: biology, radiology + defaultVersionName: '4.2' + description: The NBIA Data Retriever is an application to download radiology + images from the TCIA Radiology Portal. + package: nbia-data-retriever + url: https://wiki.cancerimagingarchive.net/display/NBIA/Current+NBIA+Data+Retriever+Help + versions: + - {description: The NBIA Data Retriever is an application to download radiology + images from the TCIA Radiology Portal., markedDefault: false, versionName: '4.2'} + - categories: biology, genomics + defaultVersionName: '2.20' + description: The bcl2fastq2 conversion software can be used to convert BCL files + from MiniSeq, MiSeq, NextSeq, HiSeq, iSeq and NovaSeq sequening systems. + package: bcl2fastq + url: https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html + versions: + - {description: 'The bcl2fastq2 conversion software can be used to convert BCL + files from MiniSeq, MiSeq, NextSeq, HiSeq, iSeq and NovaSeq sequening systems.', + markedDefault: false, versionName: '2.20'} - categories: biology, genomics defaultVersionName: 0.5.0 description: Trim Galore! is a wrapper script to automate quality and adapter @@ -5475,15 +5468,14 @@ software_modules: arch: {gpu: 1} versionName: 1.3.1 - categories: biology, genomics - defaultVersionName: '2.20' - description: The bcl2fastq2 conversion software can be used to convert BCL files - from MiniSeq, MiSeq, NextSeq, HiSeq, iSeq and NovaSeq sequening systems. - package: bcl2fastq - url: https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html + defaultVersionName: 2.3.4.1 + description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning + sequencing reads to long reference sequences. + package: bowtie2 + url: http://bowtie-bio.sourceforge.net/bowtie2 versions: - - {description: 'The bcl2fastq2 conversion software can be used to convert BCL - files from MiniSeq, MiSeq, NextSeq, HiSeq, iSeq and NovaSeq sequening systems.', - markedDefault: false, versionName: '2.20'} + - {description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning + sequencing reads to long reference sequences., markedDefault: false, versionName: 2.3.4.1} - categories: biology, genomics defaultVersionName: 3.0.2_py27 description: Assessing genome assembly and annotation completeness with Benchmarking @@ -5493,6 +5485,19 @@ software_modules: versions: - {description: Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs (BUSCO)., markedDefault: false, versionName: 3.0.2_py27} + - categories: biology, neurology + defaultVersionName: 2.4.0 + description: ANTs computes high-dimensional mappings to capture the statistics + of brain structure and function. + package: ants + url: https://stnava.github.io/ANTs + versions: + - {description: ANTs computes high-dimensional mappings to capture the statistics + of brain structure and function., markedDefault: false, versionName: 2.1.0} + - {description: ANTs computes high-dimensional mappings to capture the statistics + of brain structure and function., markedDefault: false, versionName: 2.3.1} + - {description: ANTs computes high-dimensional mappings to capture the statistics + of brain structure and function., markedDefault: false, versionName: 2.4.0} - categories: biology, genomics defaultVersionName: 1.16.1 description: Tools (written in C using htslib) for manipulating next-generation @@ -5507,36 +5512,40 @@ software_modules: - {description: Tools (written in C using htslib) for manipulating next-generation sequencing data., markedDefault: false, versionName: 1.16.1} - categories: biology, genomics - defaultVersionName: 1.1.3_py27 - description: Fit-Hi-C is a tool for assigning statistical confidence estimates - to chromosomal contact maps produced by genome architecture assays. - package: py-fithic - url: https://github.com/ay-lab/fithic - versions: - - {description: Fit-Hi-C is a tool for assigning statistical confidence estimates - to chromosomal contact maps produced by genome architecture assays., markedDefault: false, - versionName: 1.1.3_py27} - - categories: biology, neurology - defaultVersionName: 2.4.0 - description: ANTs computes high-dimensional mappings to capture the statistics - of brain structure and function. - package: ants - url: https://stnava.github.io/ANTs + defaultVersionName: '1.16' + description: BCFtools is a program for variant calling and manipulating files + in the Variant Call Format (VCF) and its binary counterpart BCF. + package: bcftools + url: https://github.com/samtools/bcftools versions: - - {description: ANTs computes high-dimensional mappings to capture the statistics - of brain structure and function., markedDefault: false, versionName: 2.1.0} - - {description: ANTs computes high-dimensional mappings to capture the statistics - of brain structure and function., markedDefault: false, versionName: 2.3.1} - - {description: ANTs computes high-dimensional mappings to capture the statistics - of brain structure and function., markedDefault: false, versionName: 2.4.0} + - {description: BCFtools is a program for variant calling and manipulating files + in the Variant Call Format (VCF) and its binary counterpart BCF., markedDefault: false, + versionName: '1.6'} + - {description: BCFtools is a program for variant calling and manipulating files + in the Variant Call Format (VCF) and its binary counterpart BCF., markedDefault: false, + versionName: '1.8'} + - {description: BCFtools is a program for variant calling and manipulating files + in the Variant Call Format (VCF) and its binary counterpart BCF., markedDefault: false, + versionName: '1.16'} - categories: biology, genomics - defaultVersionName: 3.3.1_py36 - description: Tools to process and analyze deep sequencing data. - package: py-deeptools - url: https://github.com/deeptools/deepTools/ + defaultVersionName: '202112.01' + description: Sentieon Genomics software is a set of software tools that perform + analysis of genomic data obtained from DNA sequencing. + package: sentieon + url: https://www.sentieon.com/ versions: - - {description: Tools to process and analyze deep sequencing data., markedDefault: false, - versionName: 3.3.1_py36} + - description: Sentieon Genomics software is a set of software tools that perform + analysis of genomic data obtained from DNA sequencing. + markedDefault: false + properties: + license: {restricted: 1} + versionName: '201808.01' + - description: Sentieon Genomics software is a set of software tools that perform + analysis of genomic data obtained from DNA sequencing. + markedDefault: false + properties: + license: {restricted: 1} + versionName: '202112.01' - categories: biology, neurology defaultVersionName: '20160502' description: MRIcron is a cross-platform NIfTI format image viewer. @@ -5545,16 +5554,30 @@ software_modules: versions: - {description: MRIcron is a cross-platform NIfTI format image viewer., markedDefault: false, versionName: '20160502'} - - categories: biology, genomics - defaultVersionName: 2.13.1 - description: Trinity RNA-Seq de novo transcriptome assembly. - package: trinity - url: https://github.com/trinityrnaseq/trinityrnaseq + - categories: biology, computational biology + defaultVersionName: '3.14' + description: Rosetta is the premier software suite for modeling macromolecular + structures. As a flexible, multi-purpose application, it includes tools for + structure prediction, design, and remodeling of proteins and nucleic acids. + package: rosetta + url: https://www.rosettacommons.org versions: - - {description: Trinity RNA-Seq de novo transcriptome assembly., markedDefault: false, - versionName: 2.8.4} - - {description: Trinity RNA-Seq de novo transcriptome assembly., markedDefault: false, - versionName: 2.13.1} + - description: Rosetta is the premier software suite for modeling macromolecular + structures. As a flexible, multi-purpose application, it includes tools + for structure prediction, design, and remodeling of proteins and nucleic + acids. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: '3.8' + - description: Rosetta is the premier software suite for modeling macromolecular + structures. As a flexible, multi-purpose application, it includes tools + for structure prediction, design, and remodeling of proteins and nucleic + acids. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: '3.14' - categories: biology, clinical science defaultVersionName: '20180704' description: Simvascular is a blood flow simulation and analysis toolkit. This @@ -5584,16 +5607,18 @@ software_modules: - {description: A Python framework for the analysis and visualization of trees., markedDefault: false, versionName: 3.0.0_py27} - categories: biology, genomics - defaultVersionName: 2.2.3_py39 - description: A software package for animal pose estimation. - package: py-deeplabcut - url: http://deeplabcut.org + defaultVersionName: 0.7.3 + description: Dorado is a high-performance, easy-to-use, open source basecaller + for Oxford Nanopore reads. + package: dorado + url: https://github.com/nanoporetech/dorado versions: - - description: A software package for animal pose estimation. - markedDefault: false - properties: - arch: {gpu: 1} - versionName: 2.2.3_py39 + - {description: 'Dorado is a high-performance, easy-to-use, open source basecaller + for Oxford Nanopore reads.', markedDefault: false, versionName: 0.3.4} + - {description: 'Dorado is a high-performance, easy-to-use, open source basecaller + for Oxford Nanopore reads.', markedDefault: false, versionName: 0.5.3} + - {description: 'Dorado is a high-performance, easy-to-use, open source basecaller + for Oxford Nanopore reads.', markedDefault: false, versionName: 0.7.3} - categories: biology, genomics defaultVersionName: 1.0.0 description: Longshot is a variant calling tool for diploid genomes using long @@ -5603,21 +5628,17 @@ software_modules: versions: - {description: Longshot is a variant calling tool for diploid genomes using long error prone reads., markedDefault: false, versionName: 1.0.0} - - categories: biology, computational biology - defaultVersionName: 1.84_py312 - description: Biopython is a set of freely available tools for biological computation - written in Python. - package: py-biopython - url: http://biopython.org + - categories: biology, neurology + defaultVersionName: 0.7.00 + description: BART is a toolbox for Computational Magnetic Resonance Imaging. + package: bart + url: https://mrirecon.github.io/bart/ versions: - - {description: Biopython is a set of freely available tools for biological - computation written in Python., markedDefault: false, versionName: 1.70_py27} - - {description: Biopython is a set of freely available tools for biological - computation written in Python., markedDefault: false, versionName: 1.79_py36} - - {description: Biopython is a set of freely available tools for biological - computation written in Python., markedDefault: false, versionName: 1.79_py39} - - {description: Biopython is a set of freely available tools for biological - computation written in Python., markedDefault: false, versionName: 1.84_py312} + - description: BART is a toolbox for Computational Magnetic Resonance Imaging. + markedDefault: false + properties: + arch: {gpu: 1} + versionName: 0.7.00 - categories: biology, genomics defaultVersionName: '1.8' description: A single molecule sequence assembler for genomes large and small. @@ -8069,15 +8090,6 @@ software_modules: arch: {gpu: 1} parallel: {mpi: 1} versionName: 4.0.3 - - description: The Open MPI Project is an open source Message Passing Interface - implementation that is developed and maintained by a consortium of academic, - research, and industry partners. - family: mpi - markedDefault: false - properties: - arch: {gpu: 1} - parallel: {mpi: 1} - versionName: 4.0.5 - description: The Open MPI Project is an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. diff --git a/src/docs/software/updates.xml b/src/docs/software/updates.xml index 2f9211f19..08c8479ef 100644 --- a/src/docs/software/updates.xml +++ b/src/docs/software/updates.xml @@ -5,6 +5,24 @@ Sherlock software update feed https://www.sherlock.stanford.edu/docs/software/list + + New module: biology/bases2fastq version 2.0.0 + The Bases2Fastq Software demultiplexess sequencing data from Element instruments and converts base calls into FASTQ files for secondary analysis with the FASTQ-compatible software of your choice. + https://docs.elembio.io/docs/bases2fastq + https://www.sherlock.stanford.edu/docs/software/list/?add:v=2.0.0#bases2fastq + biology, genomics + kilian@stanford.edu (Kilian Cavalotti) + Wed, 13 Nov 2024 12:45:20 -0800 + + + New module: system/munge version 0.5.16 + MUNGE (MUNGE Uid 'N' Gid Emporium) is an authentication service for creating and validating user credentials. + https://dun.github.io/munge/ + https://www.sherlock.stanford.edu/docs/software/list/?add:v=0.5.16#munge + system, tools + kilian@stanford.edu (Kilian Cavalotti) + Wed, 13 Nov 2024 12:45:20 -0800 + New version: math/cudnn version 9.4.0 NVIDIA cuDNN is a GPU-accelerated library of primitives for deep neural networks. @@ -509,14 +527,5 @@ kilian@stanford.edu (Kilian Cavalotti) Tue, 27 Aug 2024 11:16:16 -0700 - - New module: chemistry/mosaics version 1.0.0 - A collection of tools for characterizing membrane structure and dynamics within simulated trajectories of molecular systems. - https://github.com/MOSAICS-NIH/MOSAICS - https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.0.0#mosaics - chemistry, molecular dynamics - kilian@stanford.edu (Kilian Cavalotti) - Mon, 26 Aug 2024 15:24:34 -0700 -