Mercurial > repos > lecorguille > xcms_xcmsset
annotate planemo_test.sh @ 7:451ff602a957 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
author | lecorguille |
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date | Mon, 25 Apr 2016 11:14:02 -0400 |
parents | 0888f7ef739a |
children | 53923784176c |
rev | line source |
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7
451ff602a957
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
6
diff
changeset
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1 # Example of planemo command to launch test |
451ff602a957
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
6
diff
changeset
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2 |
451ff602a957
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
6
diff
changeset
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3 # Note: --galaxy_branch "dev" is set to deal with zip file |
451ff602a957
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
6
diff
changeset
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4 |
451ff602a957
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
6
diff
changeset
|
5 |
451ff602a957
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
6
diff
changeset
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6 # -- Use of installed package environments |
451ff602a957
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
6
diff
changeset
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7 # after having installing package on a local galaxy instance |
451ff602a957
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
6
diff
changeset
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8 source /w/galaxy/dev/shed_tools_tool_dependency_dir/R/3.1.2/iuc/package_r_3_1_2/1ca39eb16186/env.sh |
451ff602a957
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
6
diff
changeset
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9 source /w/galaxy/dev/shed_tools_tool_dependency_dir/bioconductor-xcms/1.44.0/lecorguille/package_bioconductor_xcms_1_44_0/0c38f7d43e08/env.sh |
451ff602a957
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
6
diff
changeset
|
10 planemo test --install_galaxy --galaxy_branch "dev" |
6
0888f7ef739a
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
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11 |
0888f7ef739a
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
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12 #All 2 test(s) executed passed. |
0888f7ef739a
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
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13 #abims_xcms_xcmsSet[0]: passed |
0888f7ef739a
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
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14 #abims_xcms_xcmsSet[1]: passed |
0888f7ef739a
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
15 |
0888f7ef739a
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
16 |
7
451ff602a957
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
6
diff
changeset
|
17 # -- Use of conda dependencies |
451ff602a957
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
6
diff
changeset
|
18 planemo conda_init --conda_prefix /tmp/mc |
451ff602a957
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
6
diff
changeset
|
19 planemo conda_install --conda_prefix /tmp/mc . |
451ff602a957
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
6
diff
changeset
|
20 planemo test --install_galaxy --conda_prefix /tmp/mc --conda_dependency_resolution --galaxy_branch "dev" |
6
0888f7ef739a
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
21 |
0888f7ef739a
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
22 #All 2 test(s) executed passed. |
0888f7ef739a
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
23 #abims_xcms_xcmsSet[0]: passed |
7
451ff602a957
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
6
diff
changeset
|
24 #abims_xcms_xcmsSet[1]: passed |
451ff602a957
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
6
diff
changeset
|
25 |
451ff602a957
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
6
diff
changeset
|
26 |
451ff602a957
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
6
diff
changeset
|
27 # -- Use of shed_test |
451ff602a957
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
6
diff
changeset
|
28 planemo shed_test --install_galaxy -t testtoolshed --galaxy_branch ="dev" |
451ff602a957
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
6
diff
changeset
|
29 |
451ff602a957
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
6
diff
changeset
|
30 #All 2 test(s) executed passed. |
451ff602a957
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
6
diff
changeset
|
31 #testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_xcmsset/2.0.8[0]: passed |
451ff602a957
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
6
diff
changeset
|
32 #testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_xcmsset/2.0.8[1]: passed |
451ff602a957
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
6
diff
changeset
|
33 |