From 73cdbddcd78d7565d21801012ea81fd2f1129f40 Mon Sep 17 00:00:00 2001
From: Jacqui Keane <drjkeane@gmail.com>
Date: Mon, 30 Nov 2020 13:15:03 +0000
Subject: [PATCH] Added software for group projects

---
 Dockerfile              |  3 +++
 build_machine.sh        |  5 ++++-
 install_dependencies.sh |  6 +++++-
 instruction_summary.txt | 19 ++++++++++++-------
 to_install.txt          |  2 ++
 5 files changed, 26 insertions(+), 9 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 35ae11c..3d71e68 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -57,6 +57,9 @@ RUN conda install wtdbg
 RUN wget https://raw.githubusercontent.com/schatzlab/genomescope/d2aefddd32ce48aa1144d9fbd80ed6b37785cd8d/genomescope.R
 RUN mv genomescope.R /miniconda/bin
 RUN chmod 754 /miniconda/bin/genomescope.R
+#Group projects
+RUN conda install freebayes
+RUN conda install gatk4
 
 # Install git
 RUN conda install git
diff --git a/build_machine.sh b/build_machine.sh
index b092668..0f8578e 100644
--- a/build_machine.sh
+++ b/build_machine.sh
@@ -58,13 +58,16 @@ conda install macs2
 conda install meme
 conda install ucsc-bedgraphtobigwig
 conda install ucsc-fetchchromsizes
-# Asembly module
+# Assembly module
 conda install assembly-stats
 conda install canu
 conda install kmer-jellyfish
 conda install seqtk
 conda install velvet
 conda install wtdbg
+# Group projects
+conda install freebayes
+conda install gatk4
 
 #Install genomescope.R (not available via bioconda)
 wget https://raw.githubusercontent.com/schatzlab/genomescope/d2aefddd32ce48aa1144d9fbd80ed6b37785cd8d/genomescope.R
diff --git a/install_dependencies.sh b/install_dependencies.sh
index c8ef137..9a56956 100644
--- a/install_dependencies.sh
+++ b/install_dependencies.sh
@@ -37,13 +37,17 @@ conda install macs2
 conda install meme
 conda install ucsc-bedgraphtobigwig
 conda install ucsc-fetchchromsizes
-# Asembly module
+# Assembly module
 conda install assembly-stats
 conda install canu
 conda install kmer-jellyfish
 conda install seqtk
 conda install velvet
 conda install wtdbg
+# Group projects
+conda install freebayes
+conda install gatk4
+
 #Install genomescope.R (not available via bioconda)
 wget ${GENOMESCOPE_DOWNLOAD_URL}
 mv genomescope.R ${MINICONDA_BIN_LOCATION}
diff --git a/instruction_summary.txt b/instruction_summary.txt
index 9509903..d8dcc16 100644
--- a/instruction_summary.txt
+++ b/instruction_summary.txt
@@ -64,30 +64,35 @@ conda install seqtk
 conda install velvet
 conda install wtdbg2
 
-12) Install genomescope (only software outside of bioconda)
+13) Install the software for group projects
+
+conda install freebayes
+conda install gatk4
+
+14) Install genomescope (only software outside of bioconda)
 
 Download the R file, move it to the bin directory and make it executable
 wget https://raw.githubusercontent.com/schatzlab/genomescope/d2aefddd32ce48aa1144d9fbd80ed6b37785cd8d/genomescope.R
 mv genomescope.R $HOME/miniconda/bin
 chmod 754 $HOME/miniconda/genomescope.R
 
-13) Install samtools last to ensure latest version is installed
+15) Install samtools last to ensure latest version is installed
 
 conda install samtools=1.10
 
-14) Install git
+16) Install git
 
 conda install git
 
-15) Install the course modules (command to be completed once the repos are ready)
+17) Install the course modules (command to be completed once the repos are ready)
 	
 git clone <repo> 
 
-16) Run a test script to check installs (tests/test_software.sh)
+18) Run a test script to check installs (tests/test_software.sh)
 
-17) Run the module test scripts (tests/test_unix.sh etc.)
+19) Run the module test scripts (tests/test_unix.sh etc.)
 
-18)Issues to address:
+20)Issues to address:
 
 Install the web browsers firefox and chrome
 Install a pdfviewer
diff --git a/to_install.txt b/to_install.txt
index eeb286e..68ede97 100644
--- a/to_install.txt
+++ b/to_install.txt
@@ -22,6 +22,8 @@ kmer-jellyfish
 seqtk
 velvet
 wtdbg
+freebayes
+gatk
 genomescope
 git
 firefox