diff --git a/awsf3-docker/Dockerfile b/awsf3-docker/Dockerfile index f8547e428..5ff9a4312 100755 --- 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 index a0a280105..fba28422a 100755 --- 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 index d2ef71ffa..a7503aa41 100644 --- 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 index f1a454d7b..1a1088911 100644 --- 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) diff --git a/tibanna/_version.py b/tibanna/_version.py index 8256eeb5c..8895f9c86 100755 --- a/tibanna/_version.py +++ b/tibanna/_version.py @@ -1,4 +1,4 @@ """Version information.""" # The following line *must* be the last in the module, exactly as formatted: -__version__ = "1.0.1" +__version__ = "1.0.2"