added java 17, 18 and fixed nextflow 22.10.7

java/17/.gitignore

@@ -0,0 +1,10 @@
+bin
+conf
+include
+jmods
+legal
+lib
+LICENSE
+man
+README
+release

java/17/README.md

@@ -0,0 +1,49 @@
+# Installation
+
+```bash
+## Commands used for installing the software
+
+MODSRC=/jhpce/shared/libd/core
+VER='17'
+mkdir -p $MODSRC/java
+cd $MODSRC/java
+wget -O- https://download.oracle.com/java/17/archive/jdk-17.0.9_linux-x64_bin.tar.gz | tar xvzf -
+mv jdk-17.0.9 $VER
+cd $VER
+## Ignore all downloaded/installed files
+echo "bin conf include jmods legal lib LICENSE man README release" | tr " " "\n" > .gitignore
+
+chmod -R a+rX $MODSRC/java/$VER
+
+## Version control files
+git add .gitignore
+git add README.md
+```
+
+# Reproducibility
+
+```bash
+## Evaluate the following commands
+module list
+date
+echo "User: ${USER}"
+echo "Hostname: ${HOSTNAME}"
+```
+
+```bash
+## copy paste the output from the previous commands
+$ module list
+
+Currently Loaded Modules:
+  1) JHPCE_ROCKY9_DEFAULT_ENV   2) JHPCE_tools/3.0
+
+$ date
+
+Mon Oct 30 01:41:44 PM EDT 2023
+
+$ echo "User: ${USER}"
+User: gpertea1
+
+$ echo "Hostname: ${HOSTNAME}"
+Hostname: compute-148.cm.cluster
+```

java/18/.gitignore

@@ -0,0 +1,10 @@
+bin
+conf
+include
+jmods
+legal
+lib
+LICENSE
+man
+README
+release

java/18/README.md

@@ -0,0 +1,48 @@
+# Installation
+
+```bash
+## Commands used for installing the software
+
+MODSRC=/jhpce/shared/libd/core
+VER='18'
+mkdir -p $MODSRC/java
+cd $MODSRC/java
+wget -O- https://download.oracle.com/java/18/archive/jdk-18.0.2.1_linux-x64_bin.tar.gz | tar xvzf -
+mv jdk-18.0.2.1 $VER
+cd $VER
+## Ignore all downloaded/installed files
+echo "bin conf include jmods legal lib LICENSE man README release" | tr " " "\n" > .gitignore
+chmod -R a+rX $MODSRC/java/$VER
+
+## Version control files
+git add .gitignore
+git add README.md
+```
+
+# Reproducibility
+
+```bash
+## Evaluate the following commands
+module list
+date
+echo "User: ${USER}"
+echo "Hostname: ${HOSTNAME}"
+```
+
+```bash
+## copy paste the output from the previous commands
+$ module list
+
+Currently Loaded Modules:
+  1) JHPCE_ROCKY9_DEFAULT_ENV   2) JHPCE_tools/3.0
+
+$ date
+
+Mon Oct 30 01:41:44 PM EDT 2023
+
+$ echo "User: ${USER}"
+User: gpertea1
+
+$ echo "Hostname: ${HOSTNAME}"
+Hostname: compute-148.cm.cluster
+```

nextflow/22.10.7/README.md

@@ -3,15 +3,15 @@
 ```bash
 ## Commands used for installing the software
 
-# At the time this command was run, the latest stable release available from
-# GitHub was 22.10.7.5853
-module load java/14.0.2
-curl -s https://get.nextflow.io | bash
-
+MODSRC=/jhpce/shared/libd/core
+VER='22.10.7'
+wget -O nextflow https://github.com/nextflow-io/nextflow/releases/download/v${VER}/nextflow-${VER}-all
+mkdir -p $MODSRC/nextflow/$VER
+mv nextflow $MODSRC/nextflow/$VER
 ## Ignore all downloaded/installed files
-echo "nextflow" > .gitignore
+#echo "nextflow" > .gitignore
 
-chmod -R 775 /jhpce/shared/jhpce/libd/nextflow/22.10.7
+chmod -R 775 $MODSRC/nextflow/$VER
 
 ## Version control files
 git add .gitignore
@@ -33,16 +33,15 @@ echo "Hostname: ${HOSTNAME}"
 $ module list
 
 Currently Loaded Modules:
-  1) matlab/R2019a     4) sge/8.1.9                       7) JHPCE_CENTOS7_DEFAULT_ENV
-  2) stata/17          5) gcc/4.4.7                       8) java/14.0.2
-  3) JHPCE_tools/1.0   6) COMMUNITY_CENTOS7_DEFAULT_ENV
+  1) JHPCE_ROCKY9_DEFAULT_ENV   2) JHPCE_tools/3.0
 
 $ date
-Fri Mar  3 15:15:32 EST 2023
+
+Mon Oct 30 01:41:44 PM EDT 2023
 
 $ echo "User: ${USER}"
-User: neagles
+User: gpertea1
 
 $ echo "Hostname: ${HOSTNAME}"
-Hostname: compute-103.cm.cluster
+Hostname: compute-148.cm.cluster
 ```