Mercurial > repos > matt-shirley > sra_tools
changeset 2:d529eff98834 draft
tool dependencies for automated sra_sdk download and compilation
| author | Matt Shirley <mdshw5@gmail.com> |
|---|---|
| date | Wed, 29 May 2013 22:10:26 -0400 |
| parents | 28fda7631857 |
| children | 326ac8ebbcdd |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 27 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed May 29 22:10:26 2013 -0400 @@ -0,0 +1,27 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="sra_toolkit" version="2.3.2-4"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.3.2-4/sra_sdk-2.3.2-4.tar.gz</action> + <action type="shell_command">make OUTDIR=$INSTALL_DIR out</action> + <action type="shell_command">make release</action> + <action type="shell_command">make</action> + <action type="shell_command">cd $INSTALL_DIR</action> + <action type="shell_command">if [[ $(uname -m) =~ x86_64 ]]; then ln -s bin64 bin; elif [[ $(uname -m) =~ i.86 ]]; then ln -s bin32 bin; fi</action> + <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$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. Various tools for working with SRA from NCBI. +This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 32 and 64 bit architectures. +Build Requirements: + ar + bash + make + gcc, g++ + libxml2 + libcurl + zlib + </readme> + </package> +</tool_dependency>