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general:computerenvironment:interpro [2019/05/16 13:17] – felixgeneral:computerenvironment:interpro [2025/05/09 06:56] (current) – [General information] freya
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-====== InterPro ======+====== InterProScan ======
 ===== General information ===== ===== General information =====
-To run InterPro locally, you need to download the InterPro databases and modify the configure file of the program. For your convenience, we prepared a ready to use version of InterProScan available at  +To run InterProScan locally, you need to download the InterPro databases and modify the configuration file of the program. As the databases are large files, this would mean a large amount of data redundancy if you were to install them individually. For this reason, we prepared a ready to use version of InterProScan with Anaconda. Environments can be shared, so you can activate the environment with: 
-<code>/share/project/interproscan-5.28-67.0</code> +<code>conda activate /home/freya/miniconda3/envs/interproscan_conda</code>
-Please run it straight from the share folder and don't attempt to copy it. Because InterProScan takes up a lot of memory, you should send this job to our cluster:+
  
-Note, that InterProScan can not create folders for the output. That means that you need to use an existing directory that does not contain special characters like dots in its name for the output.+Because InterProScan takes up a lot of memory, you should send this job to our cluster. Note, that InterProScan can not create folders for the output. That means that you need to use an existing directory that does not contain special characters like dots in its name for the output.
  
-<hidden PrerequisitesInterproScan>+/*<hidden Prerequisites InterproScan>
   - Python 2.7   - Python 2.7
     - you can check your python version with the command <code>python --version</code>     - you can check your python version with the command <code>python --version</code>
-  - Java 1.8 +  - Java 
-    - you can check your java version with the command <code>java -version</code>+    - install Java with anaconda: <WRAP><code>conda install bioconda::java-jdk</code></WRAP> 
 +  - Hmmer: ''conda install bioconda::hmmer''  
 +  - Blast: ''conda install bioconda::blast'' 
 +</hidden>*/
 **Running Interproscan** **Running Interproscan**
-<code>bash /share/project/interproscan-5.28-67.0/interproscan.sh -i <YOURINPUTFILE> -b ./interproscan -goterms -appl TIGRFAM,PRODOM,PFAM,SMART,CDD,PROSITEPROFILES,PANTHER,Coils,MobiDBLite</code>+<code>interproscan.sh -cpu 8 -i <YOURINPUTFILE> -b ./interproscan -dp -goterms -appl TIGRFAM,PANTHER,Coils,SMART,Pfam,MobiDBLite,CDD</code>
 **Options:** **Options:**
-  - **-i** - specify the input file containing the sequences in Fasta format. +  * **-i** - specify the input file containing the sequences in Fasta format. 
-  - **-b** - specify the name of the output directory +  * **-b** - specify the name of the output directory 
-  - **-goterms** - Extract the GO terms from the annotated domains and features and assigns them to the query sequence +  * **-dp** - disables using the online lookup services - all analysis are run locally 
-  - **-appl** - specify the analyses you want to include in your Interproscan run. Selecting fewer applications will speed up the search +  * **-goterms** - Extract the GO terms from the annotated domains and features and assigns them to the query sequence 
-For further information about how to run Interproscan, please see the [[https://github.com/ebi-pf-team/interproscan/wiki|online wiki]] provided by the developer. +  * **-appl** - specify the analyses you want to include in your InterProScan run. Selecting fewer applications will speed up the search 
-</hidden> +For further information about how to run InterProScan, please see the [[https://github.com/ebi-pf-team/interproscan/wiki|online wiki]] provided by the developer. 
-Once everything is set, run the analysis on all sequences. This analysis will take some time, so you best run it over the weekend.+Once everything is set, run the analysis on all sequences. This analysis will take some time, so you best run it over night.
  
-<file bash RunInterpro.sh>#!/bin/bash+<file bash RunInterpro.sh> 
 +#!/bin/bash
  
 #SBATCH --partition=all,inteli7 #SBATCH --partition=all,inteli7
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 #SBATCH --job-name="InterProTest" #SBATCH --job-name="InterProTest"
  
- +interproscan.sh -cpu 8 -i <YOURINPUTFILE> -b ./interproscan -dp -goterms -appl TIGRFAM,PANTHER,Coils,SMART,Pfam,MobiDBLite,CDD </file>  
-bash /share/project/interproscan-5.28-67.0/interproscan.sh -i <YOURINPUTFILE> -b ./interproscan -goterms -appl TIGRFAM,PRODOM,PFAM,SMART,CDD,PROSITEPROFILES,PANTHER,Coils,MobiDBLite </file>  +/*removed from inteproscan run due to failure: PROSITEPROFILES 
 +local installation that is no longer usable due to missing global installations of hmmer, java, etc.: /share/project/interproscan-5.28-67.0/interproscan.sh*/
 Just download and modify this file, then send it to the cluster with  Just download and modify this file, then send it to the cluster with 
 <code> <code>
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 </code> </code>
  
-===== Interproscan configuration ===== +/* 
-We have tweaked the configuration of interproscan a bit to improve the [[https://github.com/ebi-pf-team/interproscan/wiki/ImprovingPerformance|performance on our system]]. You will find the corresponding file at+===== InterProScan configuration ===== 
 +We have tweaked the configuration of InterProScan a bit to improve the [[https://github.com/ebi-pf-team/interproscan/wiki/ImprovingPerformance|performance on our system]]. You will find the corresponding file at
 <code> <code>
 /share/project/interproscan-5.28-67.0/interproscan.properties /share/project/interproscan-5.28-67.0/interproscan.properties
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 pirsf.pl.binary.cpu.switch=-cpu 3 pirsf.pl.binary.cpu.switch=-cpu 3
 </code> </code>
 +*/