From becd7c2b5b8126f76c045154cc88c80bffbc34e1 Mon Sep 17 00:00:00 2001 From: Carol Scott Date: Fri, 25 Nov 2022 17:31:06 +0000 Subject: [PATCH 1/3] add io_lib v1.14.14 --- recipes/io_lib/1.14.14/build.sh | 13 +++ recipes/io_lib/1.14.14/meta.yaml | 153 +++++++++++++++++++++++++++++++ 2 files changed, 166 insertions(+) create mode 100755 recipes/io_lib/1.14.14/build.sh create mode 100644 recipes/io_lib/1.14.14/meta.yaml diff --git a/recipes/io_lib/1.14.14/build.sh b/recipes/io_lib/1.14.14/build.sh new file mode 100755 index 00000000..8a151372 --- /dev/null +++ b/recipes/io_lib/1.14.14/build.sh @@ -0,0 +1,13 @@ +#!/bin/sh + +set -ex + +n="$CPU_COUNT" + +./configure \ + --prefix="$PREFIX" \ + CPPFLAGS="-I$PREFIX/include" \ + LDFLAGS="-Wl,-rpath-link,$PREFIX/lib -Wl,--disable-new-dtags -L$PREFIX/lib" + +make -j "$n" +make install diff --git a/recipes/io_lib/1.14.14/meta.yaml b/recipes/io_lib/1.14.14/meta.yaml new file mode 100644 index 00000000..79108e6c --- /dev/null +++ b/recipes/io_lib/1.14.14/meta.yaml @@ -0,0 +1,153 @@ +{% set version = "1.14.14" %} +{% set sha256 = "a471c79b9aede1776a895cb46fcb81b5d163d6ca9c3e1e33096346fef46d3598" %} + +package: + name: io_lib-pkg + version: "{{ version }}" + +about: + home: https://sourceforge.net/projects/staden + license: BSD + summary: DNA sequence assembly, editing and analysis tools. + +build: + number: 0 + +source: + url: https://github.com/jkbonfield/io_lib/releases/download/io_lib-1-14-14/io_lib-{{ version }}.tar.gz + fn: io_lib-{{ version }}.tar.gz + sha256: {{ sha256 }} + +requirements: + build: + - {{ compiler("c") }} + - autoconf + - make + host: + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libz-dev + run: + - libbz2 + - libcurl + - liblzma + - libz + +outputs: + - name: io_lib + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - autoconf + host: + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libz-dev + run: + - {{ pin_subpackage("libstaden-read", exact=True) }} + - libbz2 + - libcurl + - liblzma + - libz + files: + - bin/append_sff + - bin/convert_trace + - bin/cram_dump + - bin/cram_filter + - bin/cram_index + - bin/cram_size + - bin/extract_fastq + - bin/extract_qual + - bin/extract_seq + - bin/get_comment + - bin/hash_exp + - bin/hash_extract + - bin/hash_list + - bin/hash_sff + - bin/hash_tar + - bin/index_tar + - bin/makeSCF + - bin/scf_dump + - bin/scf_info + - bin/scf_update + - bin/scram_flagstat + - bin/scram_merge + - bin/scram_pileup + - bin/scram_test + - bin/scramble + - bin/srf2fasta + - bin/srf2fastq + - bin/srf_dump_all + - bin/srf_extract_hash + - bin/srf_extract_linear + - bin/srf_filter + - bin/srf_index_hash + - bin/srf_info + - bin/srf_list + - bin/trace_dump + - bin/ztr_dump + - share/man/man1/scramble.1 + - share/man/man1/srf2fasta.1 + - share/man/man1/srf2fastq.1 + - share/man/man1/srf_index_hash.1 + - share/man/man1/srf_info.1 + - share/man/man1/srf_list.1 + test: + commands: + - scramble -h + + - name: libstaden-read + version: {{ version }} + requirements: + build: + - {{ compiler("c") }} + - autoconf + host: + - libbz2-dev + - libcurl-dev + - liblzma-dev + - libz-dev + run: + - libbz2 + - libcurl + - liblzma + - libz + files: + - lib/libstaden-read* + test: + commands: + - test -f ${PREFIX}/lib/libstaden-read.a + - test -h ${PREFIX}/lib/libstaden-read.so + + - name: libstaden-read-dev + version: {{ version }} + requirements: + run: + - {{ pin_subpackage("libstaden-read", exact=True) }} + files: + - bin/io_lib-config + - include/io_lib + - share/man/man3/ExperimentFile.3 + - share/man/man3/exp2read.3 + - share/man/man3/fread_reading.3 + - share/man/man3/fread_scf.3 + - share/man/man3/fwrite_reading.3 + - share/man/man3/fwrite_scf.3 + - share/man/man3/read2exp.3 + - share/man/man3/read2scf.3 + - share/man/man3/read_allocate.3 + - share/man/man3/read_deallocate.3 + - share/man/man3/read_reading.3 + - share/man/man3/read_scf.3 + - share/man/man3/read_scf_header.3 + - share/man/man3/scf2read.3 + - share/man/man3/write_reading.3 + - share/man/man3/write_scf.3 + - share/man/man3/write_scf_header.3 + - share/man/man4/Read.4 + test: + commands: + - test -f ${PREFIX}/include/io_lib/cram_io.h From 2dbf1ac5f7616ab00ff3671db3ef6c3df425dcbf Mon Sep 17 00:00:00 2001 From: jmtcsngr Date: Fri, 2 Dec 2022 15:55:44 +0000 Subject: [PATCH 2/3] Update changelog for release 4.7.0 --- CHANGELOG.md | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7e861505..7af1f6d5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,21 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed +## [4.7.0] + +### Added + +#### Recipes + - io_lib 1.14.14 + +#### Features + +### Removed + +#### Recipes + +### Changed + ## [4.6.0] ### Added From 10d5fd5da4f0f564194195fe2395881e1f0884ed Mon Sep 17 00:00:00 2001 From: jmtcsngr Date: Wed, 7 Dec 2022 14:58:59 +0000 Subject: [PATCH 3/3] update versions of github actions --- .github/workflows/unit-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/unit-tests.yml b/.github/workflows/unit-tests.yml index 5c596301..312d63bc 100644 --- a/.github/workflows/unit-tests.yml +++ b/.github/workflows/unit-tests.yml @@ -16,7 +16,7 @@ jobs: COMPARE_BRANCH: "origin/devel" steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: "Initialize Miniconda" run: |