Mercurial > repos > lecorguille > xcms_fillpeaks
annotate planemo_test.sh @ 5:cd351af95d14 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
author | lecorguille |
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date | Mon, 25 Apr 2016 11:15:12 -0400 |
parents | 2edfa5e1f719 |
children | 465623d2f6fa |
rev | line source |
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5
cd351af95d14
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
4
diff
changeset
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1 # Example of planemo command to launch test |
4
2edfa5e1f719
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
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2 |
5
cd351af95d14
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
4
diff
changeset
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3 # Note: --galaxy_branch "dev" is set to deal with zip file |
4
2edfa5e1f719
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
4 |
2edfa5e1f719
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
5 |
5
cd351af95d14
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
4
diff
changeset
|
6 # -- Use of installed package environments |
cd351af95d14
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
4
diff
changeset
|
7 # after having installing package on a local galaxy instance |
4
2edfa5e1f719
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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 |
2edfa5e1f719
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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 |
2edfa5e1f719
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
10 planemo test --install_galaxy --galaxy_branch "dev" |
2edfa5e1f719
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
11 |
2edfa5e1f719
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
12 #All 1 test(s) executed passed. |
2edfa5e1f719
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
13 #abims_xcms_fillPeaks[0]: passed |
2edfa5e1f719
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
14 |
2edfa5e1f719
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
15 |
5
cd351af95d14
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
4
diff
changeset
|
16 # -- Use of conda dependencies |
cd351af95d14
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
4
diff
changeset
|
17 planemo conda_init --conda_prefix /tmp/mc |
cd351af95d14
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
4
diff
changeset
|
18 planemo conda_install --conda_prefix /tmp/mc . |
cd351af95d14
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
4
diff
changeset
|
19 planemo test --install_galaxy --conda_prefix /tmp/mc --conda_dependency_resolution --galaxy_branch "dev" |
cd351af95d14
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
4
diff
changeset
|
20 |
cd351af95d14
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
4
diff
changeset
|
21 #All 1 test(s) executed passed. |
cd351af95d14
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
4
diff
changeset
|
22 #abims_xcms_fillPeaks[0]: passed |
4
2edfa5e1f719
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
23 |
2edfa5e1f719
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
24 |
5
cd351af95d14
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
4
diff
changeset
|
25 # -- Use of shed_test |
4
2edfa5e1f719
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
26 planemo shed_test --install_galaxy --galaxy_branch "dev" -t testtoolshed |
2edfa5e1f719
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
27 #All 1 test(s) executed passed. |
2edfa5e1f719
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
|
28 #testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/2.0.6[0]: passed |