Fix/gsutil dep temp (#550)

* fixes #541 * fixes #549
Clinical-Genomics · Feb 8, 2021 · e38cd3f · e38cd3f
1 parent 0416599
commit e38cd3f
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/BALSAMIC/workflows/reference.smk b/BALSAMIC/workflows/reference.smk
@@ -171,7 +171,7 @@ rule download_reference:
             log_file = output_file + ".log"
 
             if ref.url.scheme == "gs":
-                cmd = "gsutil cp -L {} {} -".format(log_file, ref.url)
+                cmd = "export TMPDIR=/tmp; gsutil cp -L {} {} -".format(log_file, ref.url)
             else:
                 cmd = "wget -a {} -O - {}".format(log_file, ref.url)
 

diff --git a/requirements.txt b/requirements.txt
@@ -3,7 +3,7 @@ colorclass>=2.2.0
 coloredlogs>=14.0
 cyvcf2<0.10.0
 graphviz>=0.14
-gsutil>=4.50
+gsutil==4.50
 jinja2>=2.11.2
 matplotlib>=3.3.0
 networkx>=2.4
@@ -20,3 +20,4 @@ yapf>=0.30.0
 h5py>=3.1.0
 PyPDF2>=1.26.0
 markdown==3.3.3
+cryptography<3.4