comparison tool_dependencies.xml @ 3:7d6cc3605cee draft

Uploaded updated tool dependency definition.

2:b2814057f286

<?xml version="1.0"?>
<tool_dependency>
    <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" />
    </package>
    <package name="fastx_toolkit" version="0.0.13">
        <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="move_directory_files">
                        <source_directory>./bin</source_directory>
                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
                    </action>
                </actions>
                <actions>
                    <action type="download_by_url">http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit-0.0.13.tar.bz2</action>
                    <action type="set_environment_for_install">
                        <repository name="package_libgtextutils_0_6" owner="devteam" prior_installation_required="True">
                            <package name="libgtextutils" version="0.6" />
                        </repository>
                    </action>
                    <action type="shell_command">./configure --prefix=$INSTALL_DIR --disable-wall</action>
                    <action type="shell_command">make &amp;&amp; make install</action>

                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme>
        </readme>
    </package>
</tool_dependency>

3:7d6cc3605cee

<?xml version="1.0"?>
<tool_dependency>
    <package name="fastx_toolkit" version="0.0.13">
        <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="move_directory_files">
                        <source_directory>./bin</source_directory>
                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
                    </action>
                </actions>
                <actions architecture="x86_64" os="darwin">
                    <action type="download_by_url">http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_binaries_MacOSX.10.5.8_i386.tar.bz2</action>
                    <action type="move_directory_files">
                        <source_directory>./bin</source_directory>
                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
                    </action>
                </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" />
                    </package>
                    <action type="download_by_url">http://hannonlab.cshl.edu/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">
                            <package name="libgtextutils" version="0.6" />
                        </repository>
                    </action>
                    <action type="shell_command">./configure --prefix=$INSTALL_DIR --disable-wall</action>
                    <action type="shell_command">make &amp;&amp; make install</action>

                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </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>