diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index 5f365ca..dfdb1e6 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -44,7 +44,7 @@ jobs: REPO_DIR: /srv/repo # # Uncomment and modify the following line with your image name, otherwise no push will happen - # IMAGE_NAME: "/" + IMAGE_NAME: "jnywong/test-image" # Lets us monitor disks getting full as images get bigger over time - name: Show how much disk space is left diff --git a/apt.txt b/apt.txt new file mode 100644 index 0000000..b1035e1 --- /dev/null +++ b/apt.txt @@ -0,0 +1,90 @@ +# Some linux packages for basic terminal work, particularly +# oriented at users new to Unix/cmd line environments. + +# Basic unix tools +man +man-db +manpages-posix +manpages-dev +manpages-posix-dev + +# Download tools +curl +wget + +# Core text editors on a *nix box: vim and emacs +vim +emacs-nox +emacs-goodies-el + +# A couple of CLI editors that are easier than vim +# micro # currently not working on 18.04 +nano +jed +jed-extra + +# powerful terminal-based file manager, better than the one in JLab +mc + +# for easily managing multiple repositories with one command (perl-doc +# is needed for its help pages to work) +mr +perl-doc + +# Regular build tools for compiling common stuff +build-essential +gfortran + +# Dependencies for nbconvert +texlive-xetex +texlive-fonts-recommended +texlive-plain-generic +texlive-lang-chinese +lmodern + +# Other useful document-related tools +pandoc +latexdiff + +# Some useful git utilities use basic Ruby +ruby + +# Other niceties for command-line work and life +ack # powerful grep-like tool +pydf # colorized disk usage +tmux +screen +htop +nnn # cmd line file manager +zsh +rsync +tig # console UI for git +multitail +tree + +# For later, these are not available in 18.04 +#browsh # text-based web browser, occasionally handy +#dasel # json/yml/csv/etc data wrangling at the terminal +#fzf # fuzzy file finder + +## This section adds tools for desktop environment usage +dbus-x11 +xorg +xubuntu-icon-theme +xfce4 +xfce4-goodies +xclip +xsel +firefox +chromium-browser + +# GUI text editors +emacs +vim-gtk3 +gedit + +# Git clients and tools +git-gui +gitg +qgit +meld diff --git a/environment.yml b/environment.yml index 10d9a47..e69e370 100644 --- a/environment.yml +++ b/environment.yml @@ -1,16 +1,10 @@ -# This is the standard conda configuration file. Use this file to list -# the conda packages that you need installed in your environment. channels: + - bioconda - conda-forge - + - defaults dependencies: - - jupyter_contrib_nbextensions==0.5.1 - # Required until https://github.com/jupyterhub/repo2docker/pull/1196 is merged - - jupyterhub-singleuser>=3.0,<4.0 - # Set default python version to 3.10 - repo2docker sets it to 3.7 instead by default, - # which can limit us to older package versions - - python=3.10 - # Everyone wants to use nbgitpuller for everything, so let's do that - - nbgitpuller=1.1.* - # Add other packages here - # - + - fastqc=0.11.9 + - trimmomatic=0.39 + - bwa=0.7.17=ha92aebf_3 + - samtools=1.9=h8ee4bcc_1 + - bcftools=1.9 \ No newline at end of file diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..8125b99 --- /dev/null +++ b/requirements.txt @@ -0,0 +1 @@ +igv-notebook \ No newline at end of file