Mercurial > repos > iracooke > protk_trans_proteomic_pipeline
changeset 3:e85a18371516 default tip
Update
author | Ira Cooke <iracooke@gmail.com> |
---|---|
date | Sun, 09 Jun 2013 08:17:06 -0500 (2013-06-09) |
parents | cedd5e884349 |
children | |
files | README repository_dependencies.xml tool_dependencies.xml |
diffstat | 3 files changed, 26 insertions(+), 11 deletions(-) [+] |
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--- a/README Tue Mar 05 00:14:39 2013 -0500 +++ b/README Sun Jun 09 08:17:06 2013 -0500 @@ -5,16 +5,30 @@ 1. Download an install script from dropbox 2. Install several perl packages locally (inside the install directory) -3. Download the TPP source code from dropbox +3. Download the TPP source code 4. Build the TPP Intermediate files in this process are stored in ~/.protk/tmp/download and ~/.protk/tmp/build Requirements: -This package depends on the galaxy_protk -Please see instructions for that package before installing +Please see instructions for package galaxy_protk and ensure those are met + +In addition several system packages are required in order to build the TPP. The lists +below work for specific test systems. If you have a different system you may need additional packages. + +Ubuntu-12.04-LTS 64 Bit Server With OpenSSH preinstalled: + # For Building the TPP + subversion libbz2-dev swig expat libpng12-dev gnuplot libperl-dev libfuse-dev libcurl4-openssl-dev libxml2-dev libgd2-xpm-dev -In addition the following packages are required in order to build the TPP -subversion libbz2-dev swig expat libpng12-dev gnuplot libperl-dev build-essential -libgd2-xpm libfuse-dev libcurl4-openssl-dev libxml2-dev libgd2-xpm-dev + # For Installing perl modules locally (for the TPP) + liblocal-lib-perl cpanminus +Centos 6 Server + # For Building the TPP + libcurl-devel libcurl libxml2 libxml2-devel expat-devel gd gd-devel expat gnuplot libxslt swig + + # For Perl Module Management + perl-local-lib + + # On Centos you will need to install cpanminus manually with this command + curl -L http://cpanmin.us | perl - --self-upgrade
--- a/repository_dependencies.xml Tue Mar 05 00:14:39 2013 -0500 +++ b/repository_dependencies.xml Sun Jun 09 08:17:06 2013 -0500 @@ -4,5 +4,5 @@ </repositories> --> <repositories description="Requires the galaxy_protk package"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="dac478a72c1d"/> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="c25df71f7b68"/> </repositories>
--- a/tool_dependencies.xml Tue Mar 05 00:14:39 2013 -0500 +++ b/tool_dependencies.xml Sun Jun 09 08:17:06 2013 -0500 @@ -1,10 +1,13 @@ <?xml version="1.0"?> <tool_dependency> + <package name="galaxy_protk" version="1.2.2"> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="c25df71f7b68" prior_installation_required="True"/> + </package> <package name="trans_proteomic_pipeline" version="4.6.1"> <install version="1.0"> <actions> <action type="download_by_url">https://dl.dropbox.com/u/226794/galaxy_protk.tar.gz</action> - <action type="shell_command">sh install_tpp.sh $INSTALL_DIR 1.2.0</action> + <action type="shell_command">sh install_tpp.sh $INSTALL_DIR 1.2.2</action> <action type="move_file"> <source>install_tpp.sh</source> <destination>$INSTALL_DIR</destination> @@ -16,12 +19,10 @@ </actions> </install> <readme> - Compiling the TPP requires g++ subversion libbz2-dev swig expat libpng12-dev gnuplot libperl-dev libgd2-dev libgd2-xpm-dev libfuse-dev libcurl4-openssl-dev - The Trans Proteomic Pipeline is a collection of proteomics tools. For more information see http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP This package installs the TPP (Trans Proteomic Pipeline) using an installation script contained in protk. It requires the galaxy_protk package to be installed before it will work. </readme> </package> -</tool_dependency> \ No newline at end of file +</tool_dependency>