Merge pull request #25 from CCBR/chmod-perms

fix permissions issues on biowulf

.github/workflows/build.yml

@@ -30,6 +30,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip setuptools
           pip install .[dev,test]
+          python -c 'from cruise.src.util import chmod_bins_exec; chmod_bins_exec()'
       - name: Test stub run
         run: |
           cd tests/

VERSION

@@ -1 +1 @@
-0.1.0
+0.1.1-dev

bin/install_biowulf.sh

@@ -1,18 +1,23 @@
 #!/usr/bin/env bash
 set -euxo pipefail
-
 version=$1
 
-repo_path=/data/CCBR_Pipeliner/Pipelines/CRUISE/cruise-dev/
+repo_path=/data/CCBR_Pipeliner/Pipelines/CRUISE/dev/
 install_path=/data/CCBR_Pipeliner/Pipelines/CRUISE/${version}
 bin_path=${install_path}/bin/
 
 . "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh"
 conda activate py311
 
+# remove artifacts from prior builds
+pushd ${repo_path}
+rm -rf build/ *.egg-info
+popd
+
 echo "Installing CRUISE to ${install_path}"
 pip install ${repo_path} --target ${install_path} --upgrade
-chmod +x ${install_path}/cruise/bin/*.*
+chmod a+rx ${install_path}/cruise/bin/*.*
+chmod -R a+r ${install_path}
 
 if [[ ":$PATH:" != *":${bin_path}:"* ]];then
     export PATH="${PATH}:${bin_path}"

conf/biowulf.config

@@ -24,9 +24,8 @@ singularity {
     envWhitelist='https_proxy,http_proxy,ftp_proxy,DISPLAY,SLURM_JOBID,SINGULARITY_BINDPATH'
 }
 
-env {
-    SINGULARITY_CACHEDIR = "/data/CCBR_Pipeliner/SIFS"
-}
+env.SINGULARITY_CACHEDIR = "/data/CCBR_Pipeliner/SIFS"
+
 
 process.clusterOptions = ' --gres=lscratch:200 '
 process.scratch = '/lscratch/$SLURM_JOBID'

nextflow.config

@@ -84,6 +84,8 @@ env {
     R_PROFILE_USER   = "/.Rprofile"
     R_ENVIRON_USER   = "/.Renviron"
     JULIA_DEPOT_PATH = "/usr/local/share/julia"
+    // prevent python from creating pycache files
+    PYTHONDONTWRITEBYTECODE = 'true'
 }
 
 // Capture exit codes from upstream processes when piping

src/util.py

@@ -99,11 +99,12 @@ def chmod_bins_exec():
     bin_dir = nek_base("bin/")
     for filename in os.listdir(bin_dir):
         bin_path = os.path.join(bin_dir, filename)
-        file_stat = os.stat(bin_path)
-        # below is equivalent to `chmod +x`
-        os.chmod(
-            bin_path, file_stat.st_mode | stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH
-        )
+        if os.path.isfile(bin_path):
+            file_stat = os.stat(bin_path)
+            # below is equivalent to `chmod +x`
+            os.chmod(
+                bin_path, file_stat.st_mode | stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH
+            )
 
 
 class OrderedCommands(click.Group):
@@ -153,8 +154,6 @@ def run_nextflow(
 ):
     """Run a Nextflow workflow"""
     nextflow_command = ["nextflow", "run", nextfile_path]
-    # make sure bins are executable for nextflow processes
-    chmod_bins_exec()
 
     hpc = get_hpc()
     if mode == "slurm" and not hpc: