From b437cdf3a0cb6832d3beb35b00acbf5300ab5686 Mon Sep 17 00:00:00 2001
From: Nick-Eagles <nick.eagles@libd.org>
Date: Fri, 30 Jun 2023 11:24:04 -0400
Subject: [PATCH] Update READMEs for several successfully installed tools

---
 Salmon/1.2.1/README.md     | 18 +++++++-----------
 Trimmomatic/0.39/README.md | 23 ++++++++---------------
 star/2.7.8a/README.md      | 14 +++++++-------
 3 files changed, 22 insertions(+), 33 deletions(-)

diff --git a/Salmon/1.2.1/README.md b/Salmon/1.2.1/README.md
index 8881f14..7559387 100755
--- a/Salmon/1.2.1/README.md
+++ b/Salmon/1.2.1/README.md
@@ -5,10 +5,10 @@
 wget https://github.com/COMBINE-lab/salmon/releases/download/v1.2.1/Salmon-1.2.1_linux_x86_64.tar.gz
 tar xzvf Salmon-1.2.1_*.tar.gz
 rm Salmon-1.2.1_*.tar.gz
-chmod -R 775 salmon-*
+chmod -R 775 .
 
 ## Ignore all downloaded/installed files
-echo "salmon-latest_linux_x86_64/*" >> .gitignore
+echo "salmon-latest_linux_x86_64" > .gitignore
 
 ## Version control files
 git add .gitignore
@@ -30,18 +30,14 @@ echo "Hostname: ${HOSTNAME}"
 $ module list
 
 Currently Loaded Modules:
-  1) matlab/R2019a     6) COMMUNITY_CENTOS7_DEFAULT_ENV
-  2) stata/16          7) JHPCE_CENTOS7_DEFAULT_ENV
-  3) JHPCE_tools/1.0   8) conda/3-4.6.14
-  4) sge/8.1.9         9) conda_R/4.0
-  5) gcc/4.4.7
+  1) JHPCE_tools/3.0
 
-$ date
-Mon Jun 29 13:43:05 EDT 2020
+ 
 
+$ date
+Fri Jun 30 10:22:01 AM EDT 2023
 $ echo "User: ${USER}"
 User: neagles
-
 $ echo "Hostname: ${HOSTNAME}"
-Hostname: compute-075.cm.cluster
+Hostname: compute-094.cm.cluster
 ```
diff --git a/Trimmomatic/0.39/README.md b/Trimmomatic/0.39/README.md
index 968c191..3b1bee6 100755
--- a/Trimmomatic/0.39/README.md
+++ b/Trimmomatic/0.39/README.md
@@ -3,15 +3,10 @@
 ```bash
 wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.39.zip
 unzip Trimmomatic-0.39.zip
-chmod -R 755 Trimmomatic-0.39
-
-## Might help?
-ln -s /jhpce/shared/jhpce/libd/Trimmomatic/0.39/Trimmomatic-0.39/trimmomatic-0.39.jar trimmomatic.jar
+chmod -R 775 .
 
 ## Ignore all downloaded/installed files
-cat <<EOT>> .gitignore
-Trimmomatic-0.39*
-EOT
+echo Trimmomatic-0.39* > .gitignore
 
 ## Version control files
 git add .gitignore
@@ -32,17 +27,15 @@ echo "Hostname: ${HOSTNAME}"
 $ module list
 
 Currently Loaded Modules:
-  1) matlab/R2019a     4) sge/8.1.9                       7) JHPCE_CENTOS7_DEFAULT_ENV
-  2) stata/16          5) gcc/4.4.7                       8) conda/3-4.6.14
-  3) JHPCE_tools/1.0   6) COMMUNITY_CENTOS7_DEFAULT_ENV   9) conda_R/3.6
-  
-$ date
-Mon Dec  2 16:56:31 EST 2019
+  1) JHPCE_tools/3.0
+
+ 
 
+$ date
+Fri Jun 30 10:48:44 AM EDT 2023
 $ echo "User: ${USER}"
 User: neagles
-
 $ echo "Hostname: ${HOSTNAME}"
-Hostname: compute-074.cm.cluster
+Hostname: compute-094.cm.cluster
 
 ```
diff --git a/star/2.7.8a/README.md b/star/2.7.8a/README.md
index 222363d..f9c315d 100755
--- a/star/2.7.8a/README.md
+++ b/star/2.7.8a/README.md
@@ -7,9 +7,10 @@ tar -xzf 2.7.8a.tar.gz
 cd STAR-2.7.8a/source
 make
 cd ../..
+chmod -R 775 .
 
 ## Ignore all downloaded/installed files
-echo "*2.7.8a*" >> .gitignore
+echo "*2.7.8a*" > .gitignore
 
 ## Version control files
 git add .gitignore
@@ -31,15 +32,14 @@ echo "Hostname: ${HOSTNAME}"
 $ module list
 
 Currently Loaded Modules:
-  1) matlab/R2019a     5) gcc/4.4.7
-  2) stata/16          6) COMMUNITY_CENTOS7_DEFAULT_ENV
-  3) JHPCE_tools/1.0   7) JHPCE_CENTOS7_DEFAULT_ENV
-  4) sge/8.1.9
+  1) JHPCE_tools/3.0
+
+ 
 
 $ date
-Thu Mar 11 14:29:26 EST 2021
+Fri Jun 30 10:42:46 AM EDT 2023
 $ echo "User: ${USER}"
 User: neagles
 $ echo "Hostname: ${HOSTNAME}"
-Hostname: compute-079.cm.cluster
+Hostname: compute-094.cm.cluster
 ```