Mercurial > repos > yhoogstrate > edger_with_design_matrix
annotate tool_dependencies.xml @ 98:943778e4dafa draft
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 73d87531bc80b0a4e688001cd5f8ab1df9526c08-dirty
| author | yhoogstrate |
|---|---|
| date | Wed, 27 May 2015 09:25:31 -0400 |
| parents | b26040bb6301 |
| children | 6abdc14b79c2 |
| rev | line source |
|---|---|
| 24 | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | |
| 66 | 3 <package name="R" version="3.0.3"> |
| 91 | 4 <repository changeset_revision="e509651776fa" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> |
| 66 | 5 </package> |
| 24 | 6 |
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b26040bb6301
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 73d87531bc80b0a4e688001cd5f8ab1df9526c08-dirty
yhoogstrate
parents:
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7 <package name="biocLite_edgeR_limma" version="latest"> |
| 24 | 8 <install version="1.0"> |
| 9 <actions> | |
| 10 <action type="set_environment_for_install"> | |
| 91 | 11 <repository changeset_revision="e509651776fa" name="package_r_3_0_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> |
| 66 | 12 <package name="R" version="3.0.3" /> |
| 13 </repository> | |
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943778e4dafa
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 73d87531bc80b0a4e688001cd5f8ab1df9526c08-dirty
yhoogstrate
parents:
97
diff
changeset
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14 |
| 24 | 15 </action> |
| 16 <action type="make_directory">$INSTALL_DIR</action> | |
| 17 <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" > $INSTALL_DIR/runme.R</action> | |
| 18 <action type="shell_command">echo "installme=c('edgeR','limma')" >> $INSTALL_DIR/runme.R</action> | |
| 19 <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action> | |
| 20 <action type="shell_command">echo "biocLite(installme)" >> $INSTALL_DIR/runme.R</action> | |
| 21 <action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T,repos='http://cran.us.r-project.org')" >> $INSTALL_DIR/runme.R</action> | |
| 22 <action type="shell_command">echo "quit(save='no')" >> $INSTALL_DIR/runme.R</action> | |
| 23 <action type="shell_command">export PATH=$PATH && export R_HOME=$R_HOME && export R_LIBS=$R_LIBS && R CMD BATCH $INSTALL_DIR/runme.R </action> | |
| 24 </actions> | |
| 25 </install> | |
| 26 <readme> | |
| 66 | 27 Installs the latest bioc packages: edgeR & Limma |
| 24 | 28 </readme> |
| 29 </package> | |
| 30 | |
|
97
b26040bb6301
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 73d87531bc80b0a4e688001cd5f8ab1df9526c08-dirty
yhoogstrate
parents:
96
diff
changeset
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31 <package name="design_matrix_creator" version="1.0.0"> |
| 79 | 32 <install version="1.0"> |
| 33 <actions> | |
| 87 | 34 <action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/design_matrix_creator $INSTALL_DIR/bin/</action> |
| 79 | 35 <action type="chmod"> |
| 36 <file mode="755">$INSTALL_DIR/bin/design_matrix_creator</file> | |
| 37 </action> | |
| 38 <action type="set_environment"> | |
| 83 | 39 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> |
| 40 <environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable> | |
| 79 | 41 </action> |
| 42 </actions> | |
| 43 </install> | |
| 71 | 44 </package> |
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86c3aaa205b5
Added bedgraph exporting function for the DGE tables
yhoogstrate
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changeset
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45 |
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97
b26040bb6301
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 73d87531bc80b0a4e688001cd5f8ab1df9526c08-dirty
yhoogstrate
parents:
96
diff
changeset
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46 <package name="edger_dge_table_to_bedgraph" version="1.0.0"> |
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86c3aaa205b5
Added bedgraph exporting function for the DGE tables
yhoogstrate
parents:
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diff
changeset
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47 <install version="1.0"> |
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86c3aaa205b5
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yhoogstrate
parents:
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diff
changeset
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48 <actions> |
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86c3aaa205b5
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yhoogstrate
parents:
91
diff
changeset
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49 <action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/edger_dge_table_to_bedgraph $INSTALL_DIR/bin/</action> |
|
86c3aaa205b5
Added bedgraph exporting function for the DGE tables
yhoogstrate
parents:
91
diff
changeset
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50 <action type="chmod"> |
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86c3aaa205b5
Added bedgraph exporting function for the DGE tables
yhoogstrate
parents:
91
diff
changeset
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51 <file mode="755">$INSTALL_DIR/bin/edger_dge_table_to_bedgraph</file> |
|
86c3aaa205b5
Added bedgraph exporting function for the DGE tables
yhoogstrate
parents:
91
diff
changeset
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52 </action> |
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86c3aaa205b5
Added bedgraph exporting function for the DGE tables
yhoogstrate
parents:
91
diff
changeset
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53 <action type="set_environment"> |
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86c3aaa205b5
Added bedgraph exporting function for the DGE tables
yhoogstrate
parents:
91
diff
changeset
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54 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> |
|
86c3aaa205b5
Added bedgraph exporting function for the DGE tables
yhoogstrate
parents:
91
diff
changeset
|
55 <environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable> |
|
86c3aaa205b5
Added bedgraph exporting function for the DGE tables
yhoogstrate
parents:
91
diff
changeset
|
56 </action> |
|
86c3aaa205b5
Added bedgraph exporting function for the DGE tables
yhoogstrate
parents:
91
diff
changeset
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57 </actions> |
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86c3aaa205b5
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yhoogstrate
parents:
91
diff
changeset
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58 </install> |
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86c3aaa205b5
Added bedgraph exporting function for the DGE tables
yhoogstrate
parents:
91
diff
changeset
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59 </package> |
| 24 | 60 </tool_dependency> |