Mercurial > repos > lecorguille > xcms_fillpeaks

annotate planemo_test.sh @ 15:1c78d61fd646 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
author lecorguille
date Mon, 30 Jan 2017 08:52:00 -0500
parents 35269602a971
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 8
diff changeset
1 # Example of planemo command to launch test
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f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
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031eec04312c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
parents: 6
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46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 8
diff changeset
4 # -- Use of installed package environments
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 8
diff changeset
5 # after having installing package on a local galaxy instance
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031eec04312c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
parents: 6
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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
031eec04312c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
parents: 6
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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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35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 9
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8 planemo test --install_galaxy
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031eec04312c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
parents: 6
diff changeset
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031eec04312c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
parents: 6
diff changeset
10 #All 1 test(s) executed passed.
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137a69f4bcf1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 7
diff changeset
11 #abims_xcms_fillPeaks[0]: passed
137a69f4bcf1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 7
diff changeset
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137a69f4bcf1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 7
diff changeset
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46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 8
diff changeset
14 # -- Use of conda dependencies
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 8
diff changeset
15 planemo conda_init --conda_prefix /tmp/mc
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 8
diff changeset
16 planemo conda_install --conda_prefix /tmp/mc .
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35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 9
diff changeset
17 planemo test --install_galaxy --conda_prefix /tmp/mc --conda_dependency_resolution
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46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 8
diff changeset
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46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 8
diff changeset
19 #All 1 test(s) executed passed.
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 8
diff changeset
20 #abims_xcms_fillPeaks[0]: passed
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137a69f4bcf1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 7
diff changeset
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137a69f4bcf1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 7
diff changeset
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46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 8
diff changeset
23 # -- Use of shed_test
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137a69f4bcf1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 7
diff changeset
24 planemo shed_test --install_galaxy --galaxy_branch "dev" -t testtoolshed
137a69f4bcf1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 7
diff changeset
25 #All 1 test(s) executed passed.
137a69f4bcf1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 7
diff changeset
26 #testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/2.0.6[0]: passed