Mercurial > repos > ximgchess > chap_test_20230411
changeset 83:9b6e931e0de0 draft
planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
| author | ximgchess |
|---|---|
| date | Tue, 02 May 2023 15:07:28 +0000 |
| parents | 6b20bd5d489a |
| children | 1e02b5c4abdf |
| files | tomo/.test.txt.swp tomo/.tomo_reduce.bu.swp tomo/test.txt tomo/tomo_reduce.xml |
| diffstat | 4 files changed, 49 insertions(+), 1 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tomo/test.txt Tue May 02 15:07:28 2023 +0000 @@ -0,0 +1,34 @@ +I had a Galaxy tool crash repeatedly on Friday and tried a bunch of things, but nothing helped. Today I tried it from scratch and kept notes: + +Removed everything in: + /nfs/chess/galaxy-dev/var/shed_tools/testtoolshed.g2.bx.psu.edu/repos/ximgchess +and in: +/nfs/chess/galaxy-dev/var/dependencies/_conda/envs + +Rebooted the ansible + +Made sure that the repo in the testtoolshed is up to date. + +Reinstall the CHAP tool at: +https://galaxy-dev.classe.cornell.edu/admin/toolshed +Watching its progress, I can see that it first clones the tool repo and then installs the tool dependencies. +When done, I have the following new content in the galaxy tree: +ls -al /nfs/chess/galaxy-dev/var/dependencies/_conda/envs: +drwxr-xr-x 3 galaxy galaxy 32 May 1 09:17 . +drwxr-xr-x 5 galaxy galaxy 52 Apr 28 08:40 .. +drwxr-xr-x 3 galaxy galaxy 26 May 1 09:18 chap_test_20230411 + +ls -al /nfs/chess/galaxy-dev/var/shed_tools/testtoolshed.g2.bx.psu.edu/repos/ximgchess: +drwxr-xr-x 6 galaxy galaxy 317 May 1 10:04 . +drwxr-xr-x 15 galaxy galaxy 226 Aug 29 2021 .. +drwxr-xr-x 12 galaxy galaxy 184 May 1 10:03 __ChessAnalysisPipeline@0.0.2 +-rw-r--r-- 1 galaxy galaxy 0 May 1 09:18 .conda_envs_dir_test +drwxr-xr-x 27 galaxy galaxy 4096 May 1 10:02 mulled-v1-0cd3a5ccc731743d38833d0396752d8219d106c20bb3bb478c34e74608ecb1c3 +drwxr-xr-x 26 galaxy galaxy 4096 May 1 09:51 mulled-v1-67ac3841866ce74ad34393f2abb6cc61f6651a9d3f3e677b9821c88c9b0a676e +drwxr-xr-x 12 galaxy galaxy 184 May 1 10:04 mulled-v1-b1085bc9e4a5d280004f5b197e8295b3ef5167ea9ea22a074defb863f1b86458 + +When running a Galaxy tool and only when I try to pip install certif-pyspec, it bombs with: +OSError: [Errno 30] Read-only file system: '__config__.cpython-310.pyc' + +See stdout and stderr in: +/nfs/chess/aux/reduced_data/user/galaxy-dev/jobs/002/2440/outputs
--- a/tomo/tomo_reduce.xml Mon May 01 13:16:34 2023 +0000 +++ b/tomo/tomo_reduce.xml Tue May 02 15:07:28 2023 +0000 @@ -6,7 +6,21 @@ <expand macro="requirements"/> <command detect_errors="exit_code"> <![CDATA[ - $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3' + mkdir tomo_reduce_plots; + #if str($map.type_selector) == "yaml" + $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3' && + cp $input_file map.yaml && + cat $__tool_directory__/$map.detector.type_selector $tool_config > reduce.yaml && + #else + cp $input_file setup.nex && + cp $tool_config reduce.yaml && + #end if + CHAP --config + #if str($map.type_selector) == "yaml" + $__tool_directory__/pipeline_reduce_yaml.yaml + #else + $__tool_directory__/pipeline_reduce_nexus.yaml + #end if ]]> </command> <configfiles>