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interproscan-software [2015/07/02 09:26]
joguya created
interproscan-software [2019/05/28 10:43] (current)
aorth
Line 1: Line 1:
 ====== Interproscan ====== ====== Interproscan ======
 +InterPro is a database which integrates together predictive information about proteins'​ function from a number of partner resources, giving an overview of the families that a protein belongs to and the domains and sites it contains.
  
  
 ===== Information ===== ===== Information =====
  
-  * Version: 5.13+  * Version: 5.25-64.0
   * Added: July, 2015   * Added: July, 2015
-  * Updated: ​July2015 +  * Updated: ​August2017 
-  * Link: https://code.google.com/p/​interproscan/+  * Link: https://github.com/ebi-pf-team/​interproscan
  
 ===== Usage ===== ===== Usage =====
  
-Scans a range of protein signatures against your sequence.+Check for available versions: 
 <​code>​$ module avail interproscan</​code>​ <​code>​$ module avail interproscan</​code>​
  
-===== Installation ====== +Load the latest version into your environment:
-Notes from the sysadmin during installation:+
  
-<​code>​ +<​code>​$ module load interproscan/5.25-64.0</​code>​
-- requirements +
-$ module load python/2.7.+
-$ module load perl+
  
-- install interproscan +===== Installation ====== 
-$ cd /tmp/ +Notes from the sysadmin during installation:
-$ wget ftp://​ftp.ebi.ac.uk/​pub/​software/​unix/​iprscan/​5/​5.13-52.0/​interproscan-5.13-52.0-64-bit.tar.gz +
-$ wget ftp://​ftp.ebi.ac.uk/​pub/​software/​unix/​iprscan/​5/​5.13-52.0/​interproscan-5.13-52.0-64-bit.tar.gz.md5 +
-$ md5sum -c interproscan-5.13-52.0-64-bit.tar.gz.md5 +
-$ tar -xvf interproscan-5.13-52.0-64-bit.tar.gz+
  
-- install Panther models  +<​code>​$ cd /tmp 
-$ cd /tmp/​interproscan-5.13-52.0/​data +$ wget ftp://​ftp.ebi.ac.uk/​pub/​software/​unix/​iprscan/​5/​5.25-64.0/interproscan-5.25-64.0-64-bit.tar.gz 
-$ wget ftp://​ftp.ebi.ac.uk/​pub/​software/​unix/​iprscan/​5/​data/panther-data-9.0.tar.gz +$ wget ftp://​ftp.ebi.ac.uk/​pub/​software/​unix/​iprscan/​5/​5.25-64.0/interproscan-5.25-64.0-64-bit.tar.gz.md5 
-$ wget ftp://​ftp.ebi.ac.uk/​pub/​software/​unix/​iprscan/​5/​data/panther-data-9.0.tar.gz.md5 +$ md5sum -c interproscan-5.25-64.0-64-bit.tar.gz.md5 
-$ md5sum -c panther-data-9.0.tar.gz.md5 +$ tar -pxvzf interproscan-5.25-64.0-*-bit.tar.gz 
-$ tar -xvf panther-data-9.0.tar.gz+$ cd interproscan-5.25-64.0/​data 
 +$ wget ftp://​ftp.ebi.ac.uk/​pub/​software/​unix/​iprscan/​5/​data/​panther-data-11.1.tar.gz 
 +$ tar -pxvzf panther-data-11.1.tar.gz 
 +$ sudo mkdir /​export/​apps/​interproscan/​5.25-64.0 
 +$ sudo cp -r * /​export/​apps/​interproscan/​5.25-64.0</​code>​
  
-$ mkdir /​export/​apps/​interproscan/​5.13/​ +Test:
-$ mv /​tmp/​interproscan-5.13-52.0/​* /​export/​apps/​interproscan/​5.13/​+
  
-- run tests +<​code>​$ module load interproscan/​5.25-64.0 
-$ interactive +$ interproscan.sh -i /​export/​apps/​interproscan/​5.25-64.0/​test_proteins.fasta -f tsv</​code>​
-$ module load interproscan/​5.13 +
-$ interproscan.sh -i /​export/​apps/​interproscan/​5.13/​test_proteins.fasta -f tsv +
-</​code>​+
interproscan-software.1435818390.txt.gz · Last modified: 2015/07/02 09:26 by joguya