Mercurial > repos > matt-shirley > sra_tools
changeset 46:88a13a2fd23f draft
Disable caching, update descriptions, prune deprecated tools.
author | Matt Shirley <mdshw5@gmail.com> |
---|---|
date | Tue, 03 Sep 2013 22:02:30 -0400 |
parents | 3cb113532930 |
children | 04cc8176e86f |
files | fastq_dump.xml sam_dump.xml sra_fetch.py sra_fetch.xml sra_pileup.xml sra_validate.xml tool_dependencies.xml |
diffstat | 7 files changed, 13 insertions(+), 102 deletions(-) [+] |
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--- a/fastq_dump.xml Mon Aug 05 12:54:03 2013 -0400 +++ b/fastq_dump.xml Tue Sep 03 22:02:30 2013 -0400 @@ -116,6 +116,7 @@ </requirements> <help> This tool extracts reads from SRA archives using fastq-dump. + Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. The fastq-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. </help>
--- a/sam_dump.xml Mon Aug 05 12:54:03 2013 -0400 +++ b/sam_dump.xml Tue Sep 03 22:02:30 2013 -0400 @@ -92,6 +92,7 @@ </requirements> <help> This tool extracts reads from sra archives using sam-dump. + Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. The sam-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. </help>
--- a/sra_fetch.py Mon Aug 05 12:54:03 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,64 +0,0 @@ -import sys -import os -from ftplib import FTP -try: - import argparse -except ImportError: - import getopt - -def main(args): - """ Get accession number from argument """ - if module_exists('argparse'): - args = dict(vars(args)) - prefix = args['accession'][0:3] - middle = args['accession'][3:6] - suffix = args['accession'][6:9] - - ftp = FTP('ftp-trace.ncbi.nih.gov') - # Open file and transfer requested SRA as a file - # Try to change the working directory until it works - with open(args['out'], 'wb') as sra: - ftpPath = os.path.join('/sra/sra-instant/reads/ByRun/sra/', - prefix, - prefix + middle, - prefix + middle + suffix) - ftp.login('ftp') - connected = False - while not connected: - try: - ftp.cwd(ftpPath) - connected = True - except: - pass - ftp.retrbinary('RETR ' + prefix + middle + suffix + '.sra', sra.write) - ftp.quit() - -def module_exists(module_name): - try: - __import__(module_name) - except ImportError: - return False - else: - return True - -def arguments(): - parser = argparse.ArgumentParser(description="Download an SRA from the NCBI SRA FTP") - parser.add_argument('-a', '--accession', type=str, help="SRA accession ex: SRR000001") - parser.add_argument('-o', '--out', type=str, help="Name for SRA file ") - args = parser.parse_args() - return args - -if __name__ == "__main__": - if module_exists('argparse'): - args = arguments() - else: - ## fall back to getopt for python < 2.7 - args = dict() - options, remainder = getopt.getopt(sys.argv[1:], 'a:o:', ['accession=', 'out=']) - for opt, arg in options: - if opt in ('-a', '--accession'): - args['accession'] = arg - elif opt in ('-o', '--out'): - args['out'] = arg - - main(args)
--- a/sra_fetch.xml Mon Aug 05 12:54:03 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -<tool id="sra_fetch" name="Fetch SRA archive" version="1.0.3"> - <description> by accession from NCBI SRA.</description> - <command interpreter="python">sra_fetch.py --accession '$accession' --out '$output'</command> - <inputs> - <param name="accession" size="13" type="text" value="SRR000001" label="sra run accession"/> - </inputs> - <outputs> - <data format="sra" name="output" label="${accession.value}"/> - </outputs> - <help> - This tool fetches sra archives by accession from NCBI over FTP. - </help> -</tool>
--- a/sra_pileup.xml Mon Aug 05 12:54:03 2013 -0400 +++ b/sra_pileup.xml Tue Sep 03 22:02:30 2013 -0400 @@ -44,6 +44,7 @@ </requirements> <help> This tool produces pileup format from sra archives using sra-pileup. + Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. The sra-pileup program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. </help>
--- a/sra_validate.xml Mon Aug 05 12:54:03 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +0,0 @@ -<tool id="sra_validate" name="Validate sra" version="1.0.2"> - <description> and report any errors.</description> - <command>vdb-validate -md5 '$input' 2> $output </command> - <version_string>vdb-validate --version</version_string> - <inputs> - <param format="sra" name="input" type="data" label="sra archive"/> - </inputs> - <outputs> - <data format="txt" name="output"/> - </outputs> - <stdio> - <exit_code range="127" level="fatal" description="Cannot find vdb-validate binary"/> - </stdio> - <requirements> - <requirement type="package" version="2.3.2-4">sra_toolkit</requirement> - </requirements> - <help> - This tool checks the data integrity of an sra archive using vdb-validate. - The vdb-validate program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. - Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. - </help> -</tool>
--- a/tool_dependencies.xml Mon Aug 05 12:54:03 2013 -0400 +++ b/tool_dependencies.xml Tue Sep 03 22:02:30 2013 -0400 @@ -10,13 +10,16 @@ <action type="make_directory">$INSTALL_DIR/bin</action> <action type="make_directory">$INSTALL_DIR/ncbi</action> <action type="make_directory">$INSTALL_DIR/ncbi/public</action> - <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" bin64/ncbi/default.kfg</action> + <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" bin64/ncbi/default.kfg</action> <action type="shell_command">cp --recursive --dereference bin64/* $INSTALL_DIR/bin</action> <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$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 64 bit architectures. + <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: ar bash @@ -25,6 +28,10 @@ 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>