Mercurial > repos > iuc > test_permissions
changeset 2:b4f1eee85d8d draft default tip
planemo upload
| author | jmchilton |
|---|---|
| date | Sat, 04 Jul 2015 09:38:12 -0400 |
| parents | 58eb64dff5b4 |
| children | |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 78 insertions(+), 68 deletions(-) [+] |
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--- a/tool_dependencies.xml Sat Jul 04 09:36:08 2015 -0400 +++ b/tool_dependencies.xml Sat Jul 04 09:38:12 2015 -0400 @@ -1,72 +1,82 @@ -<?xml version='1.0' encoding='utf-8'?> +<?xml version="1.0"?> <tool_dependency> - <package name="blast+" version="2.2.26+"> - <install version="1.0"> - <actions_group> - <!-- Download the binaries for BLAST+ compatible with 64-bit OSX. --> - <actions os="darwin" architecture="x86_64"> - <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-universal-macosx.tar.gz</action> - <action type="move_directory_files"> - <source_directory>bin</source_directory> - <destination_directory>$INSTALL_DIR</destination_directory> - </action> - </actions> - <!-- Download the binaries for BLAST+ compatible with 32-bit OSX. --> - <actions os="darwin" architecture="i386"> - <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-universal-macosx.tar.gz</action> - <action type="move_directory_files"> - <source_directory>bin</source_directory> - <destination_directory>$INSTALL_DIR</destination_directory> - </action> - </actions> - <!-- Download the binaries for BLAST+ compatible with 64-bit Linux. --> - <actions os="linux" architecture="x86_64"> - <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-x64-linux.tar.gz</action> - <action type="move_directory_files"> - <source_directory>bin</source_directory> - <destination_directory>$INSTALL_DIR</destination_directory> - </action> - </actions> - <!-- Download the binaries for BLAST+ compatible with 32-bit Linux (i386). --> - <actions os="linux" architecture="i386"> - <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-ia32-linux.tar.gz</action> - <action type="move_directory_files"> - <source_directory>bin</source_directory> - <destination_directory>$INSTALL_DIR</destination_directory> - </action> - </actions> - <!-- Download the binaries for BLAST+ compatible with 32-bit Linux (i686). --> - <actions os="linux" architecture="i686"> - <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-ia32-linux.tar.gz</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 "Please report this via https://github.com/peterjc/galaxy_blast/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 $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. --> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> - </action> - </actions_group> - </install> + <package name="samtools" version="0.1.16"> + <install version="1.0"> + <actions_group> + <actions os="linux" architecture="i386"> + <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.16-linux-i386.tgz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <actions os="linux" architecture="x86_64"> + <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.16-linux-x86_64.tgz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <actions os="darwin" architecture="i386"> + <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.16-Darwin-i386.tgz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <actions os="darwin" architecture="x86_64"> + <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.16-Darwin-x86_64.tgz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <actions> + <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.16.tar.bz2</action> + <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>samtools</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>libbam.a</source> + <destination>$INSTALL_DIR/lib</destination> + </action> + </actions> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable> + </action> + </actions_group> + </install> <readme> -Downloads the precompiled 32bit Linux, 64bit Linux, or Mac OS X BLAST+ -binaries from the NCBI, which is faster than performing a local compliation, -avoids any issues with build dependencies, and is more reproducible between -installations as there is no variability from the compiler or library versions. - -For more details, see: -http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download + This is the last version of SAMTools to include the 'pileup' command. + + Program: samtools (Tools for alignments in the SAM format) + Version: 0.1.16 (r963:234) + + Usage: samtools <command> [options] + + Command: view SAM<->BAM conversion + sort sort alignment file + pileup generate pileup output + mpileup multi-way pileup + depth compute the depth + faidx index/extract FASTA + tview text alignment viewer + index index alignment + idxstats BAM index stats (r595 or later) + fixmate fix mate information + glfview print GLFv3 file + flagstat simple stats + calmd recalculate MD/NM tags and '=' bases + merge merge sorted alignments + rmdup remove PCR duplicates + reheader replace BAM header + cat concatenate BAMs + targetcut cut fosmid regions (for fosmid pool only) + phase phase heterozygotes </readme> - </package> + </package> </tool_dependency>