Mercurial > repos > lecorguille > xcms_group
annotate planemo_test.sh @ 9:2c1d7df89cf6 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
| author | lecorguille |
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| date | Mon, 30 Jan 2017 08:53:13 -0500 |
| parents | 0306a96cc446 |
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| rev | line source |
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0306a96cc446
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
4
diff
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1 # Example of planemo command to launch test |
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4
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
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2 |
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2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
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3 |
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5
0306a96cc446
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
4
diff
changeset
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4 # -- Use of installed package environments |
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0306a96cc446
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
4
diff
changeset
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5 # after having installing package on a local galaxy instance |
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4
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
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6 source /w/galaxy/dev/shed_tools_tool_dependency_dir/R/3.1.2/iuc/package_r_3_1_2/1ca39eb16186/env.sh |
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2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
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7 source /w/galaxy/dev/shed_tools_tool_dependency_dir/bioconductor-xcms/1.44.0/lecorguille/package_bioconductor_xcms_1_44_0/0c38f7d43e08/env.sh |
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2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
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8 planemo test --install_galaxy |
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2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
9 |
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2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
10 #All 2 test(s) executed passed. |
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2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
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11 #abims_xcms_group[0]: passed |
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2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
12 #abims_xcms_group[1]: passed |
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2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
13 |
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2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
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14 |
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5
0306a96cc446
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
4
diff
changeset
|
15 # -- Use of conda dependencies |
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0306a96cc446
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
4
diff
changeset
|
16 planemo conda_init --conda_prefix /tmp/mc |
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0306a96cc446
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
4
diff
changeset
|
17 planemo conda_install --conda_prefix /tmp/mc . |
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0306a96cc446
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
4
diff
changeset
|
18 planemo test --install_galaxy --conda_prefix /tmp/mc --conda_dependency_resolution |
|
0306a96cc446
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
4
diff
changeset
|
19 |
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0306a96cc446
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
4
diff
changeset
|
20 #All 2 test(s) executed passed. |
|
0306a96cc446
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
4
diff
changeset
|
21 #abims_xcms_group[0]: passed |
|
0306a96cc446
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
4
diff
changeset
|
22 #abims_xcms_group[1]: passed |
|
0306a96cc446
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
4
diff
changeset
|
23 |
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0306a96cc446
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
4
diff
changeset
|
24 |
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0306a96cc446
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
4
diff
changeset
|
25 # -- Use of shed_test |
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4
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
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26 planemo shed_test --install_galaxy -t testtoolshed |
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2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
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27 |
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2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
28 #All 2 test(s) executed passed. |
|
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
29 #testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/2.0.5[0]: passed |
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2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
30 #testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/2.0.5[1]: passed |