Difference between revisions of "SRA"

Latest revision as of 19:10, 27 November 2023

Description

This is the NCBI Short Read Archive Toolkit.

Note: sra will create a $HOME/ncbi/public directory and cache the prefetched data files there. However, home directory has a 40gb limit and its use for job data storage is a violation of the UFRC storage policy. You must change that location to a directory in your ufrc space before running the sra toolkit. The official approach is to use the vdb-config tool

vdb-config -i

and change the directory to, for example, /blue/$GROUP/$USER/ncbi/public. See the SRA Toolkit Configuration Documentation for more details.

Alternatively, create an 'ncbi' directory in your /blue space and symlink it to ~/ncbi. E.g.

$ mkdir /blue/mygroup/$USER/ncbi
$ ln -s /blue/mygroup/$USER/ncbi ~/ncbi

Uploads

It appears that data uploads to NCBI only work from login servers. Start a screen session before beginning an upload if there are any concerns about being disconnected.

Environment Modules

Run module spider sra to find out what environment modules are available for this application.

System Variables

HPC_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 run with a "Session Stop (Error: Client unable to connect to server (check UDP port and firewall))" error make sure you are running aspera connect on a login node. If you are already doing the transfer on a login node please submit a support request. This means that the remote site has not been allowed through the firewall. Please be sure to include the path to a script you used to run the data transfer command into the request. Do not put any sensitive information like passwords, keys, and such into the request.

@@ Line 1: / Line 1: @@
 __NOTOC__
 __NOEDITSECTION__
-[[Category:Software]]
+[[Category:Software]][[Category:Biology]][[Category:NGS]]
-<!-- ########  Template Configuration ######## -->
+{|<!--Main settings - REQUIRED-->
-<!--Edit definitions of the variables used in template calls
-Required variables:
-app - lowercase name of the application e.g. "amber"
-url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
-Optional variables:
-INTEL - Version of the Intel Compiler e.g. "11.1"
-MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
--->
-{|
-<!--Main settings - REQUIRED-->
 |{{#vardefine:app|sra}}
 |{{#vardefine:url|http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software}}
-<!--Compiler and MPI settings - OPTIONAL -->
+|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
-|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
-|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
-<!--Choose sections to enable - OPTIONAL-->
-|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
-|{{#vardefine:exe|}} <!--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 31: / Line 16: @@
 <!--Description-->
 {{#if: {{#var: url}}|
-{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}
+{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 This is the NCBI Short Read Archive Toolkit.
-''Release notes:''
+;Note: sra will create a $HOME/ncbi/public directory and cache the prefetched data files there. However, home directory has a 40gb limit and its use for job data storage is a violation of the [https://www.rc.ufl.edu/about/policies/storage/ UFRC storage policy]. You must change that location to a directory in your ufrc space before running the sra toolkit. The official approach is to use the vdb-config tool
+ vdb-config -i
-SRA Toolkit 2.1.7a includes new features in sam-dump tool and vdb-dump tools.
+and change the directory to, for example, /blue/$GROUP/$USER/ncbi/public. See the [https://github.com/ncbi/sra-tools/wiki/Toolkit-Configuration SRA Toolkit Configuration Documentation] for more details.
-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
+Alternatively, create an 'ncbi' directory in your /blue space and symlink it to ~/ncbi. E.g.
- --gzip                           Compress output using gzip
- --bzip2                          Compress output using bzip2
-vdb-dump has two new parameters
+  $ mkdir /blue/mygroup/$USER/ncbi
-  -o|--column_enum_short           enumerates columns in short form
+  $ ln -s /blue/mygroup/$USER/ncbi ~/ncbi
-  -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
+==Uploads==
-into a single script, configuration-assistant.perl that helps users download the correct references
+It appears that data uploads to NCBI only work from login servers. Start a screen session before beginning an upload if there are any concerns about being disconnected.
-for a given cSRA file and configure the user environment for the SRA Toolkit.
+<!--Modules-->
-<!--Location-->
+==Environment Modules==
-{{App_Location|app={{#var:app}}|{{#var:ver}}}}
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-Available versions:
+==System Variables==
-* 2.1.7
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
-<!-- -->
-{{#if: {{#var: mod}}|==Running the application using modules==
-{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
 * HPC_SRA_BIN - location of the executables directory
 * HPC_SRA_DOC - location of the documentation directory
-{{#if: {{#var: exe}}|==How To Run==
+<!--Additional-->
-WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
+{{#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 run with a "Session Stop (Error: Client unable to connect to server (check UDP port and firewall))"
+error ''make sure you are running aspera connect on a login node''. If you are already doing the transfer on a login node please submit a support request. This means that the remote site has not been allowed through the firewall. Please be sure to include the path to a script you used to run the data transfer command into the request. Do not put any sensitive information like passwords, keys, and such into the request.
+|}}
 {{#if: {{#var: conf}}|==Configuration==
 See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
 {{#if: {{#var: pbs}}|==PBS Script Examples==
 See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
-{{#if: {{#var: policy}}|==Usage policy==
+{{#if: {{#var: policy}}|==Usage Policy==
 WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 {{#if: {{#var: testing}}|==Performance==