Mercurial > repos > lecorguille > xcms_xcmsset

annotate planemo_test.sh @ 11:6d297efb82bc draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
author lecorguille
date Mon, 04 Jul 2016 08:43:38 -0400
parents 00ef27ba8abd
children
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00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 8
diff changeset
1 # Example of planemo command to launch test
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 8
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00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 8
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4 # -- Use of installed package environments
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 8
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5 # after having installing package on a local galaxy instance
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 8
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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
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
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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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6d297efb82bc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 10
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8 planemo test --install_galaxy
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60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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10 #All 2 test(s) executed passed.
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11 #abims_xcms_xcmsSet[0]: passed
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60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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12 #abims_xcms_xcmsSet[1]: passed
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9c3e676f7c6c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
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9c3e676f7c6c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
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00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 8
diff changeset
15 # -- Use of conda dependencies
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 8
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16 planemo conda_init --conda_prefix /tmp/mc
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 8
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17 planemo conda_install --conda_prefix /tmp/mc .
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6d297efb82bc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 10
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18 planemo test --install_galaxy --conda_prefix /tmp/mc --conda_dependency_resolution
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9c3e676f7c6c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
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9c3e676f7c6c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
parents: 6
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20 #All 2 test(s) executed passed.
9c3e676f7c6c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
parents: 6
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21 #abims_xcms_xcmsSet[0]: passed
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00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 8
diff changeset
22 #abims_xcms_xcmsSet[1]: passed
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 8
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00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 8
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00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 8
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25 # -- Use of shed_test
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6d297efb82bc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 10
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26 planemo shed_test --install_galaxy -t testtoolshed
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00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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parents: 8
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00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 8
diff changeset
28 #All 2 test(s) executed passed.
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 8
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29 #testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_xcmsset/2.0.8[0]: passed
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 8
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30 #testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_xcmsset/2.0.8[1]: passed
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 8
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