Genomics packages

.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: "<quay-username>/<repository-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

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

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

requirements.txt

@@ -0,0 +1 @@
+igv-notebook