Mercurial > repos > iuc > gatk2
comparison tool_dependencies.xml @ 6:35c00763cb5c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
| author | iuc |
|---|---|
| date | Mon, 04 Jun 2018 05:38:15 -0400 |
| parents | f244b8209eb8 |
| children |
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| 5:84584664264c | 6:35c00763cb5c |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | 2 <tool_dependency> |
| 3 <set_environment version="1.0"> | 3 <set_environment version="1.0"> |
| 4 <environment_variable action="set_to" name="GATK2_PATH">/please set the path to your GATK2 dir in the corresponding env.sh file/</environment_variable> | 4 <environment_variable action="set_to" name="GATK2_PATH">/please set the path to your GATK2 dir in the corresponding env.sh file/</environment_variable> |
| 5 </set_environment> | 5 </set_environment> |
| 6 <!-- | 6 <!-- |
| 7 Use GATK2_SITE_OPTIONS to set additional parameters that should be inserted in every GATK2 call. | 7 Use GATK2_SITE_OPTIONS to set additional parameters that should be inserted in every GATK2 call. |
| 8 The intended use case was to prohibit GATK2 to collect and send data. | 8 The intended use case was to prohibit GATK2 to collect and send data. |
| 9 For example: | 9 For example: |
| 10 | 10 |
| 11 -et "NO_ET" -K "/data/gatk2_key_file" ##ET no phone home | 11 -et "NO_ET" -K "/data/gatk2_key_file" ##ET no phone home |
| 12 --> | 12 --> |
| 13 <set_environment version="1.0"> | 13 <set_environment version="1.0"> |
| 14 <environment_variable action="set_to" name="GATK2_SITE_OPTIONS"> </environment_variable> | 14 <environment_variable action="set_to" name="GATK2_SITE_OPTIONS"> </environment_variable> |
| 15 </set_environment> | 15 </set_environment> |
| 16 | 16 |
| 17 <package name="samtools" version="0.1.19"> | 17 <package name="samtools" version="0.1.19"> |
| 18 <repository changeset_revision="923adc89c666" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> | 18 <repository changeset_revision="c9bd782f5342" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> |
| 19 </package> | 19 </package> |
| 20 <package name="picard" version="1.56.0"> | 20 <package name="picard" version="1.56.0"> |
| 21 <repository changeset_revision="61e41d21cb6f" name="package_picard_1_56_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> | 21 <repository changeset_revision="99a28567c3a3" name="package_picard_1_56_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> |
| 22 </package> | 22 </package> |
| 23 <package name="ggplot2" version="0.9.3"> | 23 <package name="ggplot2" version="0.9.3"> |
| 24 <repository changeset_revision="87a27fc31fb5" name="package_r_ggplot2_0_9_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> | 24 <repository changeset_revision="07de191649b4" name="package_r_ggplot2_0_9_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> |
| 25 </package> | 25 </package> |
| 26 </tool_dependency> | 26 </tool_dependency> |