Merge branch 'master' into metric_html_title

4dn-dcic · Feb 22, 2021 · ec04673 · ec04673
2 parents 0e3329e + 0d14059
commit ec04673
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diff --git a/awsf3-docker/Dockerfile b/awsf3-docker/Dockerfile
@@ -70,11 +70,13 @@ RUN export SINGULARITY_VERSION=3.3.0 && \
     mv singularity2 singularity
 
 # goofys
-RUN curl -O -L http://bit.ly/goofys-latest && chmod +x goofys-latest
+# RUN curl -O -L http://bit.ly/goofys-latest && chmod +x goofys-latest  # latest is not latest
+RUN wget https://github.com/kahing/goofys/releases/download/v0.24.0/goofys && chmod +x goofys
 
 # python packages
 RUN pip install boto3==1.15 awscli==1.18.152 botocore==1.18.11
 RUN pip install psutil==5.7.3
+#RUN pip install schema-salad==2.7.20180514132321 cwltool==1.0.20180525185854  # old set up, doesn't work for python3
 RUN pip install schema-salad==7.0.20200811075006 cwltool==3.0.20201017180608
 RUN pip install ec2metadata==2.0.1
 

diff --git a/awsf3-docker/run.sh b/awsf3-docker/run.sh
@@ -98,6 +98,7 @@ exl echo "## cwltool version $(cwltool --version | cut -f2 -d' ')"
 exl echo "## cromwell version $(java -jar /usr/local/bin/cromwell-35.jar --version | cut -f2 -d ' ') for WDL draft2"
 exl echo "## cromwell version $(java -jar /usr/local/bin/cromwell.jar --version | cut -f2 -d ' ') for WDL v1.0"
 exl echo "## $(singularity --version)"
+exl echo "## $(goofys --version 2>&1)"
 
 
 # getting run.json file

diff --git a/awsf3/utils.py b/awsf3/utils.py
@@ -65,7 +65,7 @@ def create_mount_command_list(mountlist_filename, runjson_input):
     with open(mountlist_filename, 'w') as f:
         for b in sorted(buckets_to_be_mounted):
             f.write("mkdir -p %s\n" % (INPUT_MOUNT_DIR_PREFIX + b))
-            f.write("goofys-latest -f %s %s &\n" % (b, INPUT_MOUNT_DIR_PREFIX + b))
+            f.write("goofys -f %s %s &\n" % (b, INPUT_MOUNT_DIR_PREFIX + b))
 
 
 def create_download_command_list(downloadlist_filename, runjson_input):

diff --git a/tests/awsf3/test_utils.py b/tests/awsf3/test_utils.py
@@ -283,9 +283,9 @@ def test_create_mount_command_list():
         mcfile_content = f.read()
 
     right_content = ('mkdir -p /data1/input-mounted-somebucket\n'
-                     'goofys-latest -f somebucket /data1/input-mounted-somebucket &\n'
+                     'goofys -f somebucket /data1/input-mounted-somebucket &\n'
                      'mkdir -p /data1/input-mounted-somebucket2\n'
-                     'goofys-latest -f somebucket2 /data1/input-mounted-somebucket2 &\n')
+                     'goofys -f somebucket2 /data1/input-mounted-somebucket2 &\n')
 
     assert mcfile_content == right_content
     os.remove(mountcommand_filename)