Mercurial > repos > peterjc > mira4_assembler
changeset 24:438d756f348b draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/mira4_assembler commit ec7b3da3689454591923d0ef3da9ab5a3c370ed4
| author | peterjc |
|---|---|
| date | Thu, 21 May 2015 11:23:43 -0400 |
| parents | ccebb3dcda88 |
| children | 55ae131c5862 |
| files | tools/mira4_assembler/README.rst tools/mira4_assembler/mira4_de_novo.xml tools/mira4_assembler/mira4_mapping.xml tools/mira4_assembler/tool_dependencies.xml |
| diffstat | 4 files changed, 5 insertions(+), 50 deletions(-) [+] |
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--- a/tools/mira4_assembler/README.rst Thu May 21 10:50:36 2015 -0400 +++ b/tools/mira4_assembler/README.rst Thu May 21 11:23:43 2015 -0400 @@ -102,6 +102,7 @@ - Reorder XML elements (internal change only). - Use the ``format_source=...`` tag in the MIRA bait wrapper. - Planemo for Tool Shed upload (``.shed.yml``, internal change only). + - MIRA 4.0.2 dependency now declared via dedicated Tool Shed package. ======= ======================================================================
--- a/tools/mira4_assembler/mira4_de_novo.xml Thu May 21 10:50:36 2015 -0400 +++ b/tools/mira4_assembler/mira4_de_novo.xml Thu May 21 11:23:43 2015 -0400 @@ -3,7 +3,7 @@ <requirements> <requirement type="binary">mira</requirement> <requirement type="binary">miraconvert</requirement> - <requirement type="package" version="4.0">MIRA</requirement> + <requirement type="package" version="4.0.2">MIRA</requirement> <requirement type="binary">samtools</requirement> <requirement type="package" version="0.1.19">samtools</requirement> </requirements>
--- a/tools/mira4_assembler/mira4_mapping.xml Thu May 21 10:50:36 2015 -0400 +++ b/tools/mira4_assembler/mira4_mapping.xml Thu May 21 11:23:43 2015 -0400 @@ -3,7 +3,7 @@ <requirements> <requirement type="binary">mira</requirement> <requirement type="binary">miraconvert</requirement> - <requirement type="package" version="4.0">MIRA</requirement> + <requirement type="package" version="4.0.2">MIRA</requirement> <requirement type="binary">samtools</requirement> <requirement type="package" version="0.1.19">samtools</requirement> </requirements>
--- a/tools/mira4_assembler/tool_dependencies.xml Thu May 21 10:50:36 2015 -0400 +++ b/tools/mira4_assembler/tool_dependencies.xml Thu May 21 11:23:43 2015 -0400 @@ -3,53 +3,7 @@ <package name="samtools" version="0.1.19"> <repository changeset_revision="0e56e4dac6e7" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> - <package name="MIRA" version="4.0"> - <install version="1.0"> - <actions_group> - <!-- Download the binaries for MIRA compatible with 64-bit OSX. --> - <actions architecture="x86_64" os="darwin"> - <action type="download_by_url">http://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0.2_darwin13.1.0_x86_64_static.tar.bz2</action> - <action type="move_directory_files"> - <source_directory>bin</source_directory> - <destination_directory>$INSTALL_DIR</destination_directory> - </action> - </actions> - <!-- Download the binaries for MIRA compatible with 64-bit Linux. --> - <actions architecture="x86_64" os="linux"> - <action type="download_by_url">http://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0.2_linux-gnu_x86_64_static.tar.bz2</action> - <action type="move_directory_files"> - <source_directory>bin</source_directory> - <destination_directory>$INSTALL_DIR</destination_directory> - </action> - </actions> - <!-- This actions tag is only processed if none of the above tags resulted in a successful installation. --> - <actions> - <action type="shell_command">echo "ERROR: Automated installation on your operating system and CPU architecture combination is not yet supported."</action> - <action type="shell_command">echo "Your machine details (the output from 'uname' and 'arch'):"</action> - <action type="shell_command">uname</action> - <action type="shell_command">arch</action> - <action type="shell_command">echo "If pre-compiled MIRA binaries are now available for this, please report this"</action> - <action type="shell_command">echo "via https://github.com/peterjc/pico_galaxyt/issues - thank you!"</action> - <action type="shell_command">false</action> - <!-- The 'false' command will return an error, so Galaxy should treat this as a failed install --> - </actions> - <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. --> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> - </action> - <action type="set_environment"> - <environment_variable action="set_to" name="MIRA4">$INSTALL_DIR</environment_variable> - </action> - </actions_group> - </install> - <readme> -Downloads MIRA v4.0.2 from Sourceforge, requesting Bastien's precompiled binaries -for 64 bit (x86_64) Linux or Mac OS X. Other platforms where compilation from -source would be required (e.g. 32 bit Linux) are not supported by this automated -installation script. - -http://chevreux.org/projects_mira.html -http://sourceforge.net/projects/mira-assembler/ - </readme> + <package name="MIRA" version="4.0.2"> + <repository changeset_revision="4be5c2deb512" name="package_mira_4_0_2" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>