...

.gitignore

@@ -3,6 +3,9 @@
 output
 logs
 nohup.out
-container.sif
+
+*.sif
+*.html
+
 .DS_Store
 .Rproj.user

scripts/container.def

@@ -20,15 +20,14 @@ From: rocker/verse:3.6.2
     apt-get update && apt-get -y install google-cloud-sdk
 
     # install python3 and snakemake
-    apt-get -y install \
-        python3 python3-pip
-    pip3 install snakemake
+    apt-get -y install python3 python3-pip
+    pip3 install snakemake==5.10.0
 
     # install bcftools
     export BCFVER=1.10.2
     apt-get -y install \
         gcc wget make zlib1g zlib1g-dev libbz2-dev liblzma-dev libcurl4-openssl-dev
-    wget https://github.com/samtools/bcftools/releases/download/1.9/bcftools-$BCFVER.tar.bz2
+    wget https://github.com/samtools/bcftools/releases/download/$BCFVER/bcftools-$BCFVER.tar.bz2
     tar -xvjf bcftools-$BCFVER.tar.bz2
     cd bcftools-$BCFVER
     ./configure --prefix=/usr/bcftools
@@ -36,21 +35,21 @@ From: rocker/verse:3.6.2
     make install
     (cd /usr/bin; ln -s /usr/bcftools/bin/bcftools bcftools)
 
-    # install PrediXcan and python dependencies (uses python 2.7)
-    apt-get -y install \
-        wget python-pip
-    wget https://raw.githubusercontent.com/hakyimlab/PrediXcan/master/Software/PrediXcan.py -O /usr/bin/predixcan
+    # download metaxcan/predixcan at exact hash and make executable
+    (cd /usr; git clone https://github.com/hakyimlab/MetaXcan; cd MetaXcan; git checkout 72e8c94edf31a4b261d29a7acf9a659804510e46)
+    ln -s /usr/MetaXcan/software/PrediXcan.py /usr/bin/predixcan
     chmod +x /usr/bin/predixcan
-    pip install \
-        argparse datetime numpy
-
-    # download, extract and store (brain) weights
-    mkdir /usr/predixcan
-    wget https://zenodo.org/record/3518299/files/mashr_eqtl.tar?download=1 -O /usr/predixcan/mashr_eqtl.tar.gz
-
+    # install dependencies
+    pip3 install numpy==1.18.1 scipy==1.4.1 pandas==1.0.1 sqlalchemy==1.3.13
+
+    # download, extract and store weights
+    mkdir -p  /usr/MetaXcan/weights
+    wget https://zenodo.org/record/3518299/files/mashr_eqtl.tar?download=1 -O /usr/MetaXcan/weights/mashr_eqtl.tar
+    tar -C /usr/MetaXcan/weights/ -xvf /usr/MetaXcan/weights/mashr_eqtl.tar
+    rm /usr/MetaXcan/weights/mashr_eqtl.tar
     # predixcan connects to the weights database with sql, needs write permission
     # even if the file system will be read only for the container
-    chmod -R 777 /usr/predixcan
+    chmod -R 777 /usr/MetaXcan
 
     # install R packages
     Rscript /tmp/install.R