Mercurial > repos > devteam > package_fastx_toolkit_0_0_13

comparison tool_dependencies.xml @ 4:e76e81b3eccf draft default tip

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Uploaded updated tool dependency recipe.
author devteam
date Tue, 24 Sep 2013 13:50:26 -0400
parents 7d6cc3605cee
children
comparison
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3:7d6cc3605cee 4:e76e81b3eccf
2 <tool_dependency> 2 <tool_dependency>
3 <package name="fastx_toolkit" version="0.0.13"> 3 <package name="fastx_toolkit" version="0.0.13">
4 <install version="1.0"> 4 <install version="1.0">
5 <actions_group> 5 <actions_group>
6 <actions architecture="x86_64" os="linux"> 6 <actions architecture="x86_64" os="linux">
7 <action type="download_by_url">http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2</action> 7 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/fastx_toolkit/0.0.13.tar.bz2</action>
8 <action type="move_directory_files"> 8 <action type="move_directory_files">
9 <source_directory>./bin</source_directory> 9 <source_directory>./bin</source_directory>
10 <destination_directory>$INSTALL_DIR/bin</destination_directory> 10 <destination_directory>$INSTALL_DIR/bin</destination_directory>
11 </action> 11 </action>
12 </actions> 12 </actions>
13 <actions architecture="i386" os="linux"> 13 <actions architecture="i386" os="linux">
14 <action type="download_by_url">http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_binaries_Linux_2.6_i686.tar.bz2</action> 14 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/i386/fastx_toolkit/0.0.13.tar.bz2</action>
15 <action type="move_directory_files"> 15 <action type="move_directory_files">
16 <source_directory>./bin</source_directory> 16 <source_directory>./bin</source_directory>
17 <destination_directory>$INSTALL_DIR/bin</destination_directory> 17 <destination_directory>$INSTALL_DIR/bin</destination_directory>
18 </action> 18 </action>
19 </actions> 19 </actions>
20 <actions architecture="i686" os="linux"> 20 <actions architecture="i686" os="linux">
21 <action type="download_by_url">http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_binaries_Linux_2.6_i686.tar.bz2</action> 21 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/i386/fastx_toolkit/0.0.13.tar.bz2</action>
22 <action type="move_directory_files"> 22 <action type="move_directory_files">
23 <source_directory>./bin</source_directory> 23 <source_directory>./bin</source_directory>
24 <destination_directory>$INSTALL_DIR/bin</destination_directory> 24 <destination_directory>$INSTALL_DIR/bin</destination_directory>
25 </action> 25 </action>
26 </actions> 26 </actions>
27 <actions architecture="i386" os="darwin"> 27 <actions architecture="i386" os="darwin">
28 <action type="download_by_url">http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_binaries_MacOSX.10.5.8_i386.tar.bz2</action> 28 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/i386/fastx_toolkit/0.0.13.tar.bz2</action>
29 <action type="move_directory_files"> 29 <action type="move_directory_files">
30 <source_directory>./bin</source_directory> 30 <source_directory>./bin</source_directory>
31 <destination_directory>$INSTALL_DIR/bin</destination_directory> 31 <destination_directory>$INSTALL_DIR/bin</destination_directory>
32 </action> 32 </action>
33 </actions> 33 </actions>
34 <actions architecture="x86_64" os="darwin"> 34 <actions architecture="x86_64" os="darwin">
35 <action type="download_by_url">http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_binaries_MacOSX.10.5.8_i386.tar.bz2</action> 35 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/fastx_toolkit/0.0.13.tar.bz2</action>
36 <action type="move_directory_files"> 36 <action type="move_directory_files">
37 <source_directory>./bin</source_directory> 37 <source_directory>./bin</source_directory>
38 <destination_directory>$INSTALL_DIR/bin</destination_directory> 38 <destination_directory>$INSTALL_DIR/bin</destination_directory>
39 </action> 39 </action>
40 </actions> 40 </actions>
41 <actions> 41 <actions>
42 <package name="libgtextutils" version="0.6"> 42 <package name="libgtextutils" version="0.6">
43 <repository changeset_revision="e28dc3aa1665" name="package_libgtextutils_0_6" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> 43 <repository changeset_revision="3f8eeecabf16" name="package_libgtextutils_0_6" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
44 </package> 44 </package>
45 <action type="download_by_url">http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit-0.0.13.tar.bz2</action> 45 <action type="download_by_url">http://depot.galaxyproject.org/package/source/fastx_toolkit/fastx_toolkit-0.0.13.tar.bz2</action>
46 <action type="set_environment_for_install"> 46 <action type="set_environment_for_install">
47 <repository changeset_revision="e28dc3aa1665" name="package_libgtextutils_0_6" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu"> 47 <repository changeset_revision="3f8eeecabf16" name="package_libgtextutils_0_6" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
48 <package name="libgtextutils" version="0.6" /> 48 <package name="libgtextutils" version="0.6" />
49 </repository> 49 </repository>
50 </action> 50 </action>
51 <action type="shell_command">./configure --prefix=$INSTALL_DIR --disable-wall</action> 51 <action type="shell_command">./configure --prefix=$INSTALL_DIR --disable-wall</action>
52 <action type="shell_command">make &amp;&amp; make install</action> 52 <action type="shell_command">make &amp;&amp; make install</action>
55 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 55 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
56 </action> 56 </action>
57 </actions_group> 57 </actions_group>
58 </install> 58 </install>
59 <readme> 59 <readme>
60 The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
61
62 Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple short-reads sequences (possibly with quality information).
63
64 The main processing of such FASTA/FASTQ files is mapping (aka aligning) the sequences to reference genomes or other databases using specialized programs. Example of such mapping programs are: Blat, SHRiMP, LastZ, MAQ and many many others.
65
66 However, it is sometimes more productive to preprocess the FASTA/FASTQ files before mapping the sequences to the genome - manipulating the sequences to produce better mapping results.
67
68 The FASTX-Toolkit tools perform some of these preprocessing tasks.
69 </readme> 60 </readme>
70 </package> 61 </package>
71 </tool_dependency> 62 </tool_dependency>