Mercurial > repos > ximgchess > chap_test_20230411

annotate tomo/test.txt @ 83:9b6e931e0de0 draft

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planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
author ximgchess
date Tue, 02 May 2023 15:07:28 +0000
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83
9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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1 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:
9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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3 Removed everything in:
9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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4 /nfs/chess/galaxy-dev/var/shed_tools/testtoolshed.g2.bx.psu.edu/repos/ximgchess
9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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5 and in:
9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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6 /nfs/chess/galaxy-dev/var/dependencies/_conda/envs
9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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8 Rebooted the ansible
9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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10 Made sure that the repo in the testtoolshed is up to date.
9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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12 Reinstall the CHAP tool at:
9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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13 https://galaxy-dev.classe.cornell.edu/admin/toolshed
9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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14 Watching its progress, I can see that it first clones the tool repo and then installs the tool dependencies.
9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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15 When done, I have the following new content in the galaxy tree:
9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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16 ls -al /nfs/chess/galaxy-dev/var/dependencies/_conda/envs:
9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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17 drwxr-xr-x 3 galaxy galaxy 32 May 1 09:17 .
9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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18 drwxr-xr-x 5 galaxy galaxy 52 Apr 28 08:40 ..
9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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19 drwxr-xr-x 3 galaxy galaxy 26 May 1 09:18 chap_test_20230411
9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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21 ls -al /nfs/chess/galaxy-dev/var/shed_tools/testtoolshed.g2.bx.psu.edu/repos/ximgchess:
9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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22 drwxr-xr-x 6 galaxy galaxy 317 May 1 10:04 .
9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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23 drwxr-xr-x 15 galaxy galaxy 226 Aug 29 2021 ..
9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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24 drwxr-xr-x 12 galaxy galaxy 184 May 1 10:03 __ChessAnalysisPipeline@0.0.2
9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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25 -rw-r--r-- 1 galaxy galaxy 0 May 1 09:18 .conda_envs_dir_test
9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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26 drwxr-xr-x 27 galaxy galaxy 4096 May 1 10:02 mulled-v1-0cd3a5ccc731743d38833d0396752d8219d106c20bb3bb478c34e74608ecb1c3
9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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27 drwxr-xr-x 26 galaxy galaxy 4096 May 1 09:51 mulled-v1-67ac3841866ce74ad34393f2abb6cc61f6651a9d3f3e677b9821c88c9b0a676e
9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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28 drwxr-xr-x 12 galaxy galaxy 184 May 1 10:04 mulled-v1-b1085bc9e4a5d280004f5b197e8295b3ef5167ea9ea22a074defb863f1b86458
9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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30 When running a Galaxy tool and only when I try to pip install certif-pyspec, it bombs with:
9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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31 OSError: [Errno 30] Read-only file system: '__config__.cpython-310.pyc'
9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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33 See stdout and stderr in:
9b6e931e0de0 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
ximgchess
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34 /nfs/chess/aux/reduced_data/user/galaxy-dev/jobs/002/2440/outputs