Mercurial > repos > mvdbeek > package_sra_toolkit_2_5_2
changeset 0:88273fd00182 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/packages/package_sra_toolkit_2_5_2 commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
author | mvdbeek |
---|---|
date | Wed, 04 Nov 2015 06:51:59 -0500 |
parents | |
children | c7f1e87de5b7 |
files | tool_dependencies.xml |
diffstat | 1 files changed, 61 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Nov 04 06:51:59 2015 -0500 @@ -0,0 +1,61 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="ascp" version="3"> + <repository changeset_revision="e109f0ec22c3" name="package_ascp_3" owner="mvdbeek" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <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="1d307129f4f2" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="ngs_sdk" version="1.1.3"> + <repository changeset_revision="2cc3f1941cb5" name="package_ngs_sdk_1_1_3" owner="mvdbeek" 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="1d307129f4f2" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="ncbi_vdb" version="2.5.2" /> + </repository> + <repository changeset_revision="2cc3f1941cb5" name="package_ngs_sdk_1_1_3" owner="mvdbeek" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="ngs_sdk" version="1.1.3" /> + </repository> + </action> + <action type="shell"> + ./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>