| Previous changeset 9:302d13490b23 (2013-11-28) Next changeset 11:02350bef2e99 (2013-12-10) |
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Commit message:
Uploaded v0.0.2 preview 2, attempt auto-install for 64 bit Mac OS X. |
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modified:
tools/mira4/mira4_bait.xml tools/mira4/tool_dependencies.xml |
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| diff -r 302d13490b23 -r 79759fdec6cb tools/mira4/mira4_bait.xml --- a/tools/mira4/mira4_bait.xml Thu Nov 28 05:07:59 2013 -0500 +++ b/tools/mira4/mira4_bait.xml Tue Dec 10 06:26:19 2013 -0500 |
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| @@ -47,7 +47,7 @@ <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" /> <param name="input_reads" value="tvc_mini.fastq" ftype="fastqsanger" /> <output name="output_reads" file="tvc_mini_bait_pos.fastq" ftype="fastqsanger" /> - </test> + </test> <test> <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" /> <param name="input_reads" value="tvc_mini.fastq" ftype="fastqsanger" /> |
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| diff -r 302d13490b23 -r 79759fdec6cb tools/mira4/tool_dependencies.xml --- a/tools/mira4/tool_dependencies.xml Thu Nov 28 05:07:59 2013 -0500 +++ b/tools/mira4/tool_dependencies.xml Tue Dec 10 06:26:19 2013 -0500 |
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| @@ -5,21 +5,45 @@ </package> <package name="MIRA" version="4.0"> <install version="1.0"> - <actions> - <action type="download_by_url">https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0rc4_linux-gnu_x86_64_static.tar.bz2</action> - <action type="move_directory_files"> - <source_directory>bin</source_directory> - <destination_directory>$INSTALL_DIR</destination_directory> + <actions_group> + <!-- Download the binaries for MIRA compatible with 64-bit OSX. --> + <actions architecture="x86_64" os="darwin"> + <action type="download_by_url">https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0rc5_darwin13.0.0_x86_64_static.tar.bz2</action> + <action type="move_directory_files"> + <source_directory>bin</source_directory> + <destination_directory>$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">https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0rc4_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> + </actions_group> </install> <readme> Downloads MIRA v4.0 from Sourceforge, requesting Bastien's precompiled binaries -for 64bit Linux (x86_64). He also has binaries for Mac OS X, which we could -use once the extensions to allow that are in the stable Galaxy releases. +for 64 bit (x86_64) Linux or Mac OS X. Other platforms were compilation from +source would be required (e.g. 32 bit Linux and Mac) are not supported by this +automated installation script. http://chevreux.org/projects_mira.html http://sourceforge.net/projects/mira-assembler/ |