fix create dir and container image

[fjrmoreews]

the bandage tools are broken (image +info) the tests scripts are here : https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2/tree/master/Assembly/bandage/test .

the issues are related to 1/ XDG_RUNTIME_DIR: $(runtime.tmpdir) dir not created .

2/ container from biocontainer (not working ?) so I created one after testing the biocontainer one's. I 'm going to email the biocontainer's container designer as well

[mr-c]

Thank you for the test data, I implemented some small fixes in https://github.com/common-workflow-library/bio-cwl-tools/pull/61 Does that work for you?

[fjrmoreews]

I still have an issue .e.g. on bandage-image: "QStandardPaths: XDG_RUNTIME_DIR points to '/tmp' which is not a directory" see the following log INFO [job bandage-image.cwl] /tmp/ycbsjeo9$ docker
run
-i
--mount=type=bind,source=/tmp/ycbsjeo9,target=/deLTHW
--mount=type=bind,source=/tmp/24qx4fa_,target=/tmp
--mount=type=bind,source=/home/fmoreews/git/cwl-workflow-SARS-CoV-2/Assembly/bandage/test/test-data/gfa.tabular,target=/var/lib/cwl/stgf0c25ba4-903e-47df-83f3-1570abcf4a8a/gfa.tabular,readonly
--workdir=/deLTHW
--read-only=true
--user=0:0
--rm
--env=TMPDIR=/tmp
--env=HOME=/deLTHW
--cidfile=/tmp/w93tlbvs/20200512142027-580051.cid
--env=QT_QPA_PLATFORM=minimal
--env=XDG_RUNTIME_DIR=/tmp
biocontainers/bandage:v0.8.1-1-deb_cv1
Bandage
image
/var/lib/cwl/stgf0c25ba4-903e-47df-83f3-1570abcf4a8a/gfa.tabular
gfa.png
--height
2500
--names
--lengths QStandardPaths: XDG_RUNTIME_DIR points to '/tmp' which is not a directory

[pvanheus]

@fjrmoreews is this PR still relevant? I tried the two tools that are currently in bio-cwl-tools and got usable outputs.