Don't store source code for programs

MIPTools.def

@@ -187,7 +187,9 @@ From: amd64/ubuntu:20.04
     ./install.sh $CPU_COUNT
 
     # install parasight
-    scp /opt/programs/parasight_v7.6/parasight.pl /opt/bin/parasight76.pl
+    cd /opt/programs
+    git clone --branch v7.6 https://github.com/bailey-lab/parasight
+    scp parasight/parasight.pl /opt/bin/parasight.pl
 
     # install basespace cli
     BS_PATH="https://launch.basespace.illumina.com/CLI/latest/amd64-linux/bs"

docs/CHANGELOG.rst

@@ -32,6 +32,8 @@ Bug Fixes
 Maintenance
 -----------
 
+-  Install programs from GitHub instead of storing source code
+   (:github:user:`arisp99`, :github:pull:`36`).
 -  Update LICENSE year.
 -  Store containers using an HTTP directory (:github:issue:`12`).
 -  Remove duplicated files.

docs/requirements.txt

@@ -5,6 +5,6 @@ readthedocs-sphinx-search==0.1.1
 docutils==0.16 # see https://github.com/sphinx-doc/sphinx/issues/9049
 myst_parser==0.15.2 # write docs using MyST (a flavor of markdown)
 sphinx_copybutton==0.4.0 # copy button
-sphinx-toolbox==2.18.0 # many useful tools for sphinx
+sphinx-toolbox==2.18.2 # many useful tools for sphinx
 sphinx-licenseinfo==0.3.0 # license info
 sphinx-notfound-page==0.8 # 404 page

programs/README.md

@@ -0,0 +1,8 @@
+# Programs
+
+This folder can be used to install custom software into the MIPTools container.
+By placing software into this folder, the software will be built into the
+container. Currently only the
+[`bcl2fastq`](https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html)
+software, which is used for demultiplexing BCL files, can be installed. Consult
+the documentation for additional instruction.