Mercurial > repos > devteam > package_fastx_toolkit_0_0_13

comparison tool_dependencies.xml @ 3:7d6cc3605cee draft

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Uploaded updated tool dependency definition.
author devteam
date Tue, 10 Sep 2013 16:41:48 -0400
parents b2814057f286
children e76e81b3eccf
comparison
equal deleted inserted replaced
2:b2814057f286 3:7d6cc3605cee
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="libgtextutils" version="0.6">
4 <repository changeset_revision="e28dc3aa1665" name="package_libgtextutils_0_6" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="fastx_toolkit" version="0.0.13"> 3 <package name="fastx_toolkit" version="0.0.13">
7 <install version="1.0"> 4 <install version="1.0">
8 <actions_group> 5 <actions_group>
9 <actions architecture="x86_64" os="linux"> 6 <actions architecture="x86_64" os="linux">
10 <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://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2</action>
32 <action type="move_directory_files"> 29 <action type="move_directory_files">
33 <source_directory>./bin</source_directory> 30 <source_directory>./bin</source_directory>
34 <destination_directory>$INSTALL_DIR/bin</destination_directory> 31 <destination_directory>$INSTALL_DIR/bin</destination_directory>
35 </action> 32 </action>
36 </actions> 33 </actions>
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>
36 <action type="move_directory_files">
37 <source_directory>./bin</source_directory>
38 <destination_directory>$INSTALL_DIR/bin</destination_directory>
39 </action>
40 </actions>
37 <actions> 41 <actions>
42 <package name="libgtextutils" version="0.6">
43 <repository changeset_revision="e28dc3aa1665" name="package_libgtextutils_0_6" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
44 </package>
38 <action type="download_by_url">http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit-0.0.13.tar.bz2</action> 45 <action type="download_by_url">http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit-0.0.13.tar.bz2</action>
39 <action type="set_environment_for_install"> 46 <action type="set_environment_for_install">
40 <repository name="package_libgtextutils_0_6" owner="devteam" prior_installation_required="True"> 47 <repository changeset_revision="e28dc3aa1665" name="package_libgtextutils_0_6" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
41 <package name="libgtextutils" version="0.6" /> 48 <package name="libgtextutils" version="0.6" />
42 </repository> 49 </repository>
43 </action> 50 </action>
44 <action type="shell_command">./configure --prefix=$INSTALL_DIR --disable-wall</action> 51 <action type="shell_command">./configure --prefix=$INSTALL_DIR --disable-wall</action>
45 <action type="shell_command">make &amp;&amp; make install</action> 52 <action type="shell_command">make &amp;&amp; make install</action>
48 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 55 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
49 </action> 56 </action>
50 </actions_group> 57 </actions_group>
51 </install> 58 </install>
52 <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.
53 </readme> 69 </readme>
54 </package> 70 </package>
55 </tool_dependency> 71 </tool_dependency>