...

Merge branch 'refactor-gtex-v8' of https://git.center-tbi.eu/kunzmann/impute-gene-expression into refactor-gtex-v8

# Conflicts:
#	scripts/container.def

scripts/container.def

@@ -20,9 +20,8 @@ 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
@@ -38,7 +37,7 @@ From: rocker/verse:3.6.2
 
     # install MetaXcan and python dependencies
     mkdir -p /usr/MetaXcan
-    (cd /usr/MetaXcan; git clone https://github.com/hakyimlab/MetaXcan; cd MetaXcan; git checkout b5a1741244c32a30cd16d5eca5da4d0f38bc90a7)
+    (cd /usr; git clone https://github.com/hakyimlab/MetaXcan; cd MetaXcan; git checkout b5a1741244c32a30cd16d5eca5da4d0f38bc90a7)
     ln -s /usr/MetaXcan/software/PrediXcan.py /usr/bin/predixcan
     chmod +x /usr/bin/predixcan
     pip3 install \
@@ -49,8 +48,9 @@ From: rocker/verse:3.6.2
     apt-get -y install wget
     mkdir /usr/MetaXcan/weights
     wget https://zenodo.org/record/3518299/files/mashr_eqtl.tar?download=1 \
-        -O /usr/MetaXcan/weights/mashr_eqtl.tar.gz
-    [todo untar]
+        -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