Mercurial > repos > devteam > package_fastx_toolkit_0_0_13

diff tool_dependencies.xml @ 4:e76e81b3eccf draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded updated tool dependency recipe.
author devteam
date Tue, 24 Sep 2013 13:50:26 -0400
parents 7d6cc3605cee
children
line wrap: on
line diff
--- a/tool_dependencies.xml	Tue Sep 10 16:41:48 2013 -0400
+++ b/tool_dependencies.xml	Tue Sep 24 13:50:26 2013 -0400
@@ -4,35 +4,35 @@
         <install version="1.0">
             <actions_group>
                 <actions architecture="x86_64" os="linux">
-                    <action type="download_by_url">http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2</action>
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/fastx_toolkit/0.0.13.tar.bz2</action>
                     <action type="move_directory_files">
                         <source_directory>./bin</source_directory>
                         <destination_directory>$INSTALL_DIR/bin</destination_directory>
                     </action>
                 </actions>
                 <actions architecture="i386" os="linux">
-                    <action type="download_by_url">http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_binaries_Linux_2.6_i686.tar.bz2</action>
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/i386/fastx_toolkit/0.0.13.tar.bz2</action>
                     <action type="move_directory_files">
                         <source_directory>./bin</source_directory>
                         <destination_directory>$INSTALL_DIR/bin</destination_directory>
                     </action>
                 </actions>
                 <actions architecture="i686" os="linux">
-                    <action type="download_by_url">http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_binaries_Linux_2.6_i686.tar.bz2</action>
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/i386/fastx_toolkit/0.0.13.tar.bz2</action>
                     <action type="move_directory_files">
                         <source_directory>./bin</source_directory>
                         <destination_directory>$INSTALL_DIR/bin</destination_directory>
                     </action>
                 </actions>
                 <actions architecture="i386" os="darwin">
-                    <action type="download_by_url">http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_binaries_MacOSX.10.5.8_i386.tar.bz2</action>
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/i386/fastx_toolkit/0.0.13.tar.bz2</action>
                     <action type="move_directory_files">
                         <source_directory>./bin</source_directory>
                         <destination_directory>$INSTALL_DIR/bin</destination_directory>
                     </action>
                 </actions>
                 <actions architecture="x86_64" os="darwin">
-                    <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>
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/fastx_toolkit/0.0.13.tar.bz2</action>
                     <action type="move_directory_files">
                         <source_directory>./bin</source_directory>
                         <destination_directory>$INSTALL_DIR/bin</destination_directory>
@@ -40,11 +40,11 @@
                 </actions>
                 <actions>
                     <package name="libgtextutils" version="0.6">
-                        <repository changeset_revision="e28dc3aa1665" name="package_libgtextutils_0_6" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+                        <repository changeset_revision="3f8eeecabf16" name="package_libgtextutils_0_6" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
                     </package>
-                    <action type="download_by_url">http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit-0.0.13.tar.bz2</action>
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/source/fastx_toolkit/fastx_toolkit-0.0.13.tar.bz2</action>
                     <action type="set_environment_for_install">
-                        <repository changeset_revision="e28dc3aa1665" name="package_libgtextutils_0_6" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <repository changeset_revision="3f8eeecabf16" name="package_libgtextutils_0_6" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
                             <package name="libgtextutils" version="0.6" />
                         </repository>
                     </action>
@@ -57,15 +57,6 @@
             </actions_group>
         </install>
         <readme>
-The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
-
-Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple short-reads sequences (possibly with quality information).
-
-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.
-
-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.
-
-The FASTX-Toolkit tools perform some of these preprocessing tasks. 
         </readme>
     </package>
 </tool_dependency>