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general:computerenvironment:interpro [2025/05/08 09:54] – freyageneral:computerenvironment:interpro [2025/05/09 06:56] (current) – [General information] freya
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   - Hmmer: ''conda install bioconda::hmmer''    - Hmmer: ''conda install bioconda::hmmer'' 
   - Blast: ''conda install bioconda::blast''   - Blast: ''conda install bioconda::blast''
-*/+</hidden>*/
 **Running Interproscan** **Running Interproscan**
-<code>interproscan.sh -cpu 8 -i <YOURINPUTFILE> -b ./interproscan -goterms -appl TIGRFAM,PANTHER,Coils,SMART,Pfam,MobiDBLite,CDD</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 
 +  * **-appl** - specify the analyses you want to include in your InterProScan run. Selecting fewer applications will speed up the search
 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. 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.
-</hidden> 
 Once everything is set, run the analysis on all sequences. This analysis will take some time, so you best run it over night. Once everything is set, run the analysis on all sequences. This analysis will take some time, so you best run it over night.
  
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 #SBATCH --job-name="InterProTest" #SBATCH --job-name="InterProTest"
  
-interproscan.sh -cpu 8 -i <YOURINPUTFILE> -b ./interproscan -goterms -appl TIGRFAM,PANTHER,Coils,SMART,Pfam,MobiDBLite,CDD </file> +interproscan.sh -cpu 8 -i <YOURINPUTFILE> -b ./interproscan -dp -goterms -appl TIGRFAM,PANTHER,Coils,SMART,Pfam,MobiDBLite,CDD </file> 
 /*removed from inteproscan run due to failure: PROSITEPROFILES /*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*/ 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*/