Mercurial > repos > iuc > package_sra_toolkit_2_5_2
changeset 0:ab06c0240705 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
author | iuc |
---|---|
date | Sun, 06 Dec 2015 09:04:27 -0500 |
parents | |
children | bb51af9130ea |
files | tool_dependencies.xml |
diffstat | 1 files changed, 60 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sun Dec 06 09:04:27 2015 -0500 @@ -0,0 +1,60 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="perl" version="5.18.1"> + <repository changeset_revision="8b3509930a44" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="ncbi_vdb" version="2.5.2"> + <repository changeset_revision="b980182ad267" name="package_ncbi_vdb_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="ngs_sdk" version="1.1.3"> + <repository changeset_revision="1197d3c98375" name="package_ngs_sdk_1_1_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="sra_toolkit" version="2.5.2"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action> + <action type="set_environment_for_install"> + <repository changeset_revision="8b3509930a44" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="perl" version="5.18.1" /> + </repository> + <repository changeset_revision="b980182ad267" name="package_ncbi_vdb_2_5_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="ncbi_vdb" version="2.5.2" /> + </repository> + <repository changeset_revision="1197d3c98375" name="package_ngs_sdk_1_1_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="ngs_sdk" version="1.1.3" /> + </repository> + </action> + <action type="shell_command"> + ./configure --prefix=$INSTALL_DIR -with-ngs-sdk-prefix=$NGS_SDK_DIR --with-ncbi-vdb-sources=$NCBI_VDB_DIR --with-ncbi-vdb-build=$NCBI_VDB_DIR --build=$INSTALL_DIR/build + </action> + <action type="shell_command"> + sed -i -e "109s/-static//" tools/copycat/Makefile + </action> + <action type="make_install" /> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> + Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives. + This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures. + When running on Amazon EC2, be sure to keep in mind the size limitation of EBS storage devices when requesting a + download of a large SRA data set. + + Build Requirements: + - make + - git + - gcc + - g++ + - libxml2 + - libcurl4 + - zlib + + On a debian based Linux OS use: + + apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev + + </readme> + </package> +</tool_dependency>