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planemo upload
author jmchilton
date Sat, 04 Jul 2015 09:38:12 -0400
parents 58eb64dff5b4
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1:58eb64dff5b4 2:b4f1eee85d8d
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="blast+" version="2.2.26+"> 3 <package name="samtools" version="0.1.16">
4 <install version="1.0"> 4 <install version="1.0">
5 <actions_group> 5 <actions_group>
6 <!-- Download the binaries for BLAST+ compatible with 64-bit OSX. --> 6 <actions os="linux" architecture="i386">
7 <actions os="darwin" architecture="x86_64"> 7 <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>
8 <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> 8 <action type="move_directory_files">
9 <action type="move_directory_files"> 9 <source_directory>.</source_directory>
10 <source_directory>bin</source_directory> 10 <destination_directory>$INSTALL_DIR</destination_directory>
11 <destination_directory>$INSTALL_DIR</destination_directory> 11 </action>
12 </action> 12 </actions>
13 </actions> 13 <actions os="linux" architecture="x86_64">
14 <!-- Download the binaries for BLAST+ compatible with 32-bit OSX. --> 14 <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>
15 <actions os="darwin" architecture="i386"> 15 <action type="move_directory_files">
16 <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> 16 <source_directory>.</source_directory>
17 <action type="move_directory_files"> 17 <destination_directory>$INSTALL_DIR</destination_directory>
18 <source_directory>bin</source_directory> 18 </action>
19 <destination_directory>$INSTALL_DIR</destination_directory> 19 </actions>
20 </action> 20 <actions os="darwin" architecture="i386">
21 </actions> 21 <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>
22 <!-- Download the binaries for BLAST+ compatible with 64-bit Linux. --> 22 <action type="move_directory_files">
23 <actions os="linux" architecture="x86_64"> 23 <source_directory>.</source_directory>
24 <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> 24 <destination_directory>$INSTALL_DIR</destination_directory>
25 <action type="move_directory_files"> 25 </action>
26 <source_directory>bin</source_directory> 26 </actions>
27 <destination_directory>$INSTALL_DIR</destination_directory> 27 <actions os="darwin" architecture="x86_64">
28 </action> 28 <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>
29 </actions> 29 <action type="move_directory_files">
30 <!-- Download the binaries for BLAST+ compatible with 32-bit Linux (i386). --> 30 <source_directory>.</source_directory>
31 <actions os="linux" architecture="i386"> 31 <destination_directory>$INSTALL_DIR</destination_directory>
32 <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-ia32-linux.tar.gz</action> 32 </action>
33 <action type="move_directory_files"> 33 </actions>
34 <source_directory>bin</source_directory> 34 <actions>
35 <destination_directory>$INSTALL_DIR</destination_directory> 35 <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.16.tar.bz2</action>
36 </action> 36 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
37 </actions> 37 <action type="shell_command">make</action>
38 <!-- Download the binaries for BLAST+ compatible with 32-bit Linux (i686). --> 38 <action type="move_file">
39 <actions os="linux" architecture="i686"> 39 <source>samtools</source>
40 <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> 40 <destination>$INSTALL_DIR/bin</destination>
41 <action type="move_directory_files"> 41 </action>
42 <source_directory>bin</source_directory> 42 <action type="move_file">
43 <destination_directory>$INSTALL_DIR</destination_directory> 43 <source>libbam.a</source>
44 </action> 44 <destination>$INSTALL_DIR/lib</destination>
45 </actions> 45 </action>
46 <!-- This actions tag is only processed if none of the above tags resulted in a successful installation. --> 46 </actions>
47 <actions> 47 <action type="set_environment">
48 <action type="shell_command">echo "ERROR: Automated installation on your operating system and CPU architecture combination is not yet supported."</action> 48 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
49 <action type="shell_command">echo "Your machine details (the output from 'uname' and 'arch'):"</action> 49 <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable>
50 <action type="shell_command">uname</action> 50 </action>
51 <action type="shell_command">arch</action> 51 </actions_group>
52 <action type="shell_command">echo "Please report this via https://github.com/peterjc/galaxy_blast/issues - thank you!"</action> 52 </install>
53 <action type="shell_command">false</action>
54 <!-- The 'false' command will return an error, so Galaxy should treat this as a failed install -->
55 </actions>
56 <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. -->
57 <action type="set_environment">
58 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
59 </action>
60 </actions_group>
61 </install>
62 <readme> 53 <readme>
63 Downloads the precompiled 32bit Linux, 64bit Linux, or Mac OS X BLAST+ 54 This is the last version of SAMTools to include the 'pileup' command.
64 binaries from the NCBI, which is faster than performing a local compliation, 55
65 avoids any issues with build dependencies, and is more reproducible between 56 Program: samtools (Tools for alignments in the SAM format)
66 installations as there is no variability from the compiler or library versions. 57 Version: 0.1.16 (r963:234)
67 58
68 For more details, see: 59 Usage: samtools &lt;command&gt; [options]
69 http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastDocs&amp;DOC_TYPE=Download 60
61 Command: view SAM&lt;-&gt;BAM conversion
62 sort sort alignment file
63 pileup generate pileup output
64 mpileup multi-way pileup
65 depth compute the depth
66 faidx index/extract FASTA
67 tview text alignment viewer
68 index index alignment
69 idxstats BAM index stats (r595 or later)
70 fixmate fix mate information
71 glfview print GLFv3 file
72 flagstat simple stats
73 calmd recalculate MD/NM tags and '=' bases
74 merge merge sorted alignments
75 rmdup remove PCR duplicates
76 reheader replace BAM header
77 cat concatenate BAMs
78 targetcut cut fosmid regions (for fosmid pool only)
79 phase phase heterozygotes
70 </readme> 80 </readme>
71 </package> 81 </package>
72 </tool_dependency> 82 </tool_dependency>