Difference between revisions of "SRA"

Revision as of 19:55, 10 August 2012

Description

This is the NCBI Short Read Archive Toolkit.

Release notes:

SRA Toolkit 2.1.7a includes new features in sam-dump tool and vdb-dump tools.

Sam-dump now supports slicing across multiple sequences, and dumping cSRA files to fasta and fastq formats. In addition, sam-dump has three new parameters:

-=|--hide-identical              Output '=' if base is identical to reference
--gzip                           Compress output using gzip
--bzip2                          Compress output using bzip2

vdb-dump has two new parameters

-o|--column_enum_short           enumerates columns in short form
-b|--boolean                     defines how boolean's are printed (1,T)

We have combined the functionality of two scripts, config-assistant.perl and reference-assistant.perl into a single script, configuration-assistant.perl that helps users download the correct references for a given cSRA file and configure the user environment for the SRA Toolkit.

Required Modules

modules documentation

Serial

sra

System Variables

HPC_{{#uppercase:sra}}_DIR - installation directory
HPC_SRA_BIN - location of the executables directory
HPC_SRA_DOC - location of the documentation directory

Additional Information

Aspera Connect

To download SRA data you can use the "ascp" utility from the Aspera Connect browser plugin package. We have a copy installed and provided by the sra module. A wrapper script ascp.sh that automatically uses the ssh key is available. For instance:

ascp.sh -QT anonftp@ftp-private.ncbi.nlm.nih.gov:/genomes/Bacteria/all.faa.tar.gz faa

will download the all.faa.tar.gz archive to the faa directory.

Note: if the download fails to start on the first try with a "Session Stop (Error: Client unable to connect to server (check UDP port and firewall))" error just re-run the command. It's a DNS (host name resolution) problem, which will resolve itself.

@@ Line 5: / Line 5: @@
 |{{#vardefine:app|sra}}
 |{{#vardefine:url|http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software}}
-|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
+|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
 |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
 |{{#vardefine:pbs|}} <!--Enable PBS script wiki page link-->
@@ Line 39: / Line 39: @@
 into a single script, configuration-assistant.perl that helps users download the correct references
 for a given cSRA file and configure the user environment for the SRA Toolkit.
-<!--Location-->
 <!--Modules-->
 ==Required Modules==
@@ Line 45: / Line 44: @@
 ===Serial===
 *{{#var:app}}
+==System Variables==
+* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
 * HPC_SRA_BIN - location of the executables directory
 * HPC_SRA_DOC - location of the documentation directory
+<!--Additional-->
-==Aspera Connect==
+{{#if: {{#var: exe}}|==Additional Information==
+===Aspera Connect===
 To download SRA data you can use the "ascp" utility from the [http://asperasoft.com/downloads/ Aspera Connect] browser plugin package. We have a copy installed and provided by the sra module. A wrapper script ''ascp.sh'' that automatically uses the ssh key is available. For instance:
   ascp.sh -QT anonftp@ftp-private.ncbi.nlm.nih.gov:/genomes/Bacteria/all.faa.tar.gz faa
 will download the all.faa.tar.gz archive to the faa directory.
 '''Note:''' if the download fails to start on the first try with a "Session Stop (Error: Client unable to connect to server (check UDP port and firewall))"
 error just re-run the command. It's a DNS (host name resolution) problem, which will resolve itself.
-{{#if: {{#var: exe}}|==How To Run==
+|}}
-WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
 {{#if: {{#var: conf}}|==Configuration==
 See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}