Mercurial > repos > devteam > package_fastx_toolkit_0_0_13

changeset 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
files tool_dependencies.xml
diffstat 1 files changed, 8 insertions(+), 17 deletions(-) [+]
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>