adding leafcutter conda module building instructions and conda env/se…

…ssion info files

leafcutter/.gitignore

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+leafcutter*/*

leafcutter/README.md

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+# Installation
+
+This uses the module conda/3-24 to benefit for using the libmamba solver.
+
+```bash
+module load conda/3-24
+conda create /jhpce/shared/libd/core/leafcutter/leafcutter-0.2.9 --solver=libmamba python=3.10 r-base=4.0.5 radian 
+conda activate /jhpce/shared/libd/core/leafcutter/leafcutter-0.2.9
+```
+To prevent unexpected upgrades to newer versions of R, which seem to break leafcutter installation, we pin the R version:
+
+```bash
+echo "r-base 4.0.*" >> /jhpce/shared/libd/core/leafcutter/leafcutter-0.2.9/conda-meta/pinned
+```
+
+Then we install various pre-built packagesa for this R version.
+
+```bash
+conda install r-devtools r-rstantools numpy scipy scikit-learn
+conda install -c bioconda bioconductor-biobase bioconductor-dirichletmultinomial bioconductor-summarizedexperiment \
+ bioconductor-edger bioconductor-limma bioconductor-deseq2 bioconductor-rtracklayer
+```
+
+Then, in an R session:
+
+```R
+devtools::install_github("davidaknowles/leafcutter/leafcutter")
+```
+
+For convenience (and access to the other scripts related to the leafcutter workflow), I also cloned the leafcutter repository:
+```bash
+cd /jhpce/shared/libd/core/leafcutter/leafcutter-0.2.9
+git clone https://github.com/davidaknowles/leafcutter.git
+# for convenience also copy some programs related to the leafcutter workflow
+cp ~gpertea1/sw/bin/{samtools,regtools,bedtools,bgzip} bin/
+cp leafcutter/{clustering,scripts}/*.{py,pl,R,sh} bin/
+# save current environment and session info 
+conda export > leafcutter-0.2.9.yaml
+R -e 'library(leafcutter);sessionInfo()' > sessionInfo.txt
+```
+
+Set the proper permissions and version control files
+```bash
+cd /jhpce/shared/libd/core/leafcutter
+echo "leafcutter*/*" > .gitignore
+chmod -R a+rX .
+git add .gitignore README.md sessionInfo.txt leafcutter-0.2.9.yaml leafcutter-0.2.9/conda-meta/pinned
+```