From b89967bf076cb3b9a1727ffe25215806a62996d6 Mon Sep 17 00:00:00 2001
From: Nick-Eagles <nick.eagles@libd.org>
Date: Mon, 28 Aug 2023 14:20:41 -0400
Subject: [PATCH] Remove uninstalled and outdated versions of some modules
---
cell2location/0.8a0/.gitignore | 1 -
cell2location/0.8a0/README.md | 65 ----------------------------------
hisat2/2.0.4/.gitignore | 1 -
hisat2/2.0.4/README.md | 44 -----------------------
hisat2/2.0.5/.gitignore | 1 -
hisat2/2.0.5/README.md | 44 -----------------------
htslib/1.13/.gitignore | 4 ---
htslib/1.13/README.md | 53 ---------------------------
samtools/1.17/.gitignore | 3 --
samtools/1.17/README.md | 51 --------------------------
10 files changed, 267 deletions(-)
delete mode 100755 cell2location/0.8a0/.gitignore
delete mode 100755 cell2location/0.8a0/README.md
delete mode 100755 hisat2/2.0.4/.gitignore
delete mode 100755 hisat2/2.0.4/README.md
delete mode 100755 hisat2/2.0.5/.gitignore
delete mode 100755 hisat2/2.0.5/README.md
delete mode 100755 htslib/1.13/.gitignore
delete mode 100755 htslib/1.13/README.md
delete mode 100755 samtools/1.17/.gitignore
delete mode 100755 samtools/1.17/README.md
diff --git a/cell2location/0.8a0/.gitignore b/cell2location/0.8a0/.gitignore
deleted file mode 100755
index 943a3f8..0000000
--- a/cell2location/0.8a0/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-cell2location_env
diff --git a/cell2location/0.8a0/README.md b/cell2location/0.8a0/README.md
deleted file mode 100755
index fa9bd24..0000000
--- a/cell2location/0.8a0/README.md
+++ /dev/null
@@ -1,65 +0,0 @@
-# Installation
-
-```bash
-## Commands used for installing the software
-
-# This installation follows:
-# https://github.com/BayraktarLab/cell2location#conda-environment-for-a100-gpus,
-# creating a CUDA-aware cell2location installation the authors recommend for
-# A100 GPUs (the GPUs available on the caracol node). The following commands
-# were executed on the caracol node.
-
-# Make sure not to rely on user packages
-export PYTHONNOUSERSITE="not_a_real_path"
-
-# Create a conda environment containing cell2location
-conda create -y -p $PWD/cell2location_env python=3.9
-conda activate $PWD/cell2location_env
-conda install -y -c anaconda hdf5 pytables git
-pip install scvi-tools
-pip install git+https://github.com/BayraktarLab/cell2location.git#egg=cell2location[tutorials]
-pip3 install torch==1.11.0+cu113 torchvision==0.12.0+cu113 torchaudio==0.11.0 -f https://download.pytorch.org/whl/torch_stable.html
-conda deactivate
-
-## Ignore all downloaded/installed files
-echo "cell2location_env" >> .gitignore
-
-# Allow fairly relaxed permissions, but protect against accidental changes to
-# the conda environment
-chmod -R 775 /jhpce/shared/jhpce/libd/cell2location
-chmod -R 755 /jhpce/shared/jhpce/libd/cell2location/0.8a0/cell2location_env
-
-## 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) matlab/R2019a 3) JHPCE_tools/1.0 5) gcc/4.4.7 7) JHPCE_CENTOS7_DEFAULT_ENV
- 2) stata/17 4) sge/8.1.9 6) COMMUNITY_CENTOS7_DEFAULT_ENV
-
-
-
-$ date
-Thu Apr 28 15:22:41 EDT 2022
-
-$ echo "User: ${USER}"
-User: neagles
-
-$ echo "Hostname: ${HOSTNAME}"
-Hostname: compute-126.cm.cluster
-```
diff --git a/hisat2/2.0.4/.gitignore b/hisat2/2.0.4/.gitignore
deleted file mode 100755
index c55feb3..0000000
--- a/hisat2/2.0.4/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-hisat2-2.0.4*
diff --git a/hisat2/2.0.4/README.md b/hisat2/2.0.4/README.md
deleted file mode 100755
index d49aef8..0000000
--- a/hisat2/2.0.4/README.md
+++ /dev/null
@@ -1,44 +0,0 @@
-# Installation
-
-```bash
-## Commands used for installing the software
-wget ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.0.4-Linux_x86_64.zip
-unzip hisat2-2.0.4-Linux_x86_64.zip
-chmod -R 755 hisat2-2.0.4
-
-## Ignore all downloaded/installed files
-echo "hisat2-2.0.4*" > .gitignore
-
-## 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_DEFAULT_ENV 4) JHPCE_tools/1.0 7) conda_R/3.5
- 2) matlab/R2017b 5) COMMUNITY_DEFAULT_ENV 8) gcc/4.4.7
- 3) stata/15 6) sge/2011.11p1 9) git/2.17.0
-
-
-
-$ date
-Tue Oct 23 16:14:12 EDT 2018
-$ echo "User: ${USER}"
-User: lcollado
-$ echo "Hostname: ${HOSTNAME}"
-Hostname: compute-060
-```
diff --git a/hisat2/2.0.5/.gitignore b/hisat2/2.0.5/.gitignore
deleted file mode 100755
index dfee41d..0000000
--- a/hisat2/2.0.5/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-hisat2-2.0.5*
diff --git a/hisat2/2.0.5/README.md b/hisat2/2.0.5/README.md
deleted file mode 100755
index 215a036..0000000
--- a/hisat2/2.0.5/README.md
+++ /dev/null
@@ -1,44 +0,0 @@
-# Installation
-
-```bash
-## Commands used for installing the software
-wget ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.0.5-Linux_x86_64.zip
-unzip hisat2-2.0.5-Linux_x86_64.zip
-chmod -R 755 hisat2-2.0.5
-
-## Ignore all downloaded/installed files
-echo "hisat2-2.0.5*" > .gitignore
-
-## 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_DEFAULT_ENV 4) JHPCE_tools/1.0 7) conda_R/3.5
- 2) matlab/R2017b 5) COMMUNITY_DEFAULT_ENV 8) gcc/4.4.7
- 3) stata/15 6) sge/2011.11p1 9) git/2.17.0
-
-
-
-$ date
-Tue Oct 23 17:03:59 EDT 2018
-$ echo "User: ${USER}"
-User: lcollado
-$ echo "Hostname: ${HOSTNAME}"
-Hostname: compute-060
-```
diff --git a/htslib/1.13/.gitignore b/htslib/1.13/.gitignore
deleted file mode 100755
index f864629..0000000
--- a/htslib/1.13/.gitignore
+++ /dev/null
@@ -1,4 +0,0 @@
-htslib*
-bin
-share
-lib
diff --git a/htslib/1.13/README.md b/htslib/1.13/README.md
deleted file mode 100755
index ed31bc9..0000000
--- a/htslib/1.13/README.md
+++ /dev/null
@@ -1,53 +0,0 @@
-# Installation
-
-```bash
-## Commands used for installing the software
-wget https://github.com/samtools/htslib/releases/download/1.13/htslib-1.13.tar.bz2 -O htslib-1.13.tar.bz2 && \
- tar -xjvf htslib-1.13.tar.bz2 && \
- cd htslib-1.13 && \
- ./configure prefix=/jhpce/shared/jhpce/libd/htslib/1.13 && \
- make && \
- make install
-
-## Ignore all downloaded/installed files
-cd ..
-echo "htslib*" > .gitignore
-echo "bin" >> .gitignore
-echo "share" >> .gitignore
-echo "lib" >> .gitignore
-
-## Set permissions
-chmod -R 775 .
-
-## 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) matlab/R2021a 3) JHPCE_tools/1.0 5) gcc/4.4.7 7) JHPCE_CENTOS7_DEFAULT_ENV 9) git/2.28.0 11) ruby/2.6.4p104 13) conda/3-4.6.14
- 2) stata/16 4) sge/8.1.9 6) COMMUNITY_CENTOS7_DEFAULT_ENV 8) git-status-size/github 10) git-lfs/2.8.0 12) rmate/1.5.9 14) conda_R/4.1
-
-
-
-$ date
-Wed Sep 1 16:39:09 EDT 2021
-$ echo "User: ${USER}"
-User: lcollado
-$ echo "Hostname: ${HOSTNAME}"
-Hostname: compute-104.cm.cluste
-```
diff --git a/samtools/1.17/.gitignore b/samtools/1.17/.gitignore
deleted file mode 100755
index be7c1f2..0000000
--- a/samtools/1.17/.gitignore
+++ /dev/null
@@ -1,3 +0,0 @@
-samtools*
-bin
-share
diff --git a/samtools/1.17/README.md b/samtools/1.17/README.md
deleted file mode 100755
index b4933d8..0000000
--- a/samtools/1.17/README.md
+++ /dev/null
@@ -1,51 +0,0 @@
-# Installation
-
-```bash
-## Commands used for installing the software
-wget https://github.com/samtools/samtools/releases/download/1.17/samtools-1.17.tar.bz2 -O samtools.tar.bz2
-tar -xjf samtools.tar.bz2
-cd samtools-1.17
-./configure prefix=/jhpce/shared/jhpce/libd/samtools/1.17
-make
-make install
-
-## Ignore all downloaded/installed files
-echo "samtools*" > .gitignore
-echo "bin" >> .gitignore
-echo "share" >> .gitignore
-
-chmod -R 775 /jhpce/shared/jhpce/libd/samtools/1.17
-
-## 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) matlab/R2019a 4) sge/8.1.9 7) JHPCE_CENTOS7_DEFAULT_ENV
- 2) stata/17 5) gcc/4.4.7
- 3) JHPCE_tools/1.0 6) COMMUNITY_CENTOS7_DEFAULT_ENV
-
-
-
-$ date
-Wed May 10 10:39:40 EDT 2023
-$ echo "User: ${USER}"
-User: neagles
-$ echo "Hostname: ${HOSTNAME}"
-Hostname: compute-107.cm.cluster
-```