Layers/Functional-annotations.md

@@ -16,6 +16,7 @@ title: Functional annotations
 
 
 
+
 Functional annotation helps bringing biological meaning to genetic sequences. Functional annotation is usually obtained through protein sequence similarity. Indeed, across two organisms, if two sequences are very similar, one can infer that they can encode for the same biological function.
 There are several main parameters that will impact the process of functional annotation:
 - how distant is the species which was actually annotated with experimental data (the reference)
@@ -152,26 +153,13 @@ md5sum -c interproscan-5.65-97.0-bit.tar.gz.md5
 
 ./interproscan-5.65-97.0/interproscan.sh -cpu 15 -iprlookup -goterms -f TSV -i mtrun.fa -o mtru.tsv
 ```
-In case of error, using a docker container can be a solution.
-```
-docker pull interpro/interproscan:5.65-97.0
-docker run --rm \
-    -v $PWD/interproscan-5.65-97.0/data:/opt/interproscan/data \ # mount the data dir of interproscan
-    -v $PWD/input:/input \ # mount the input local dir containing the protein files
-    -v $PWD/results:/output \
-    -v $PWD/temp:/temp \
-    interpro/interproscan:5.65-97.0 \
-    --input /input/proteins/mtrun_prot.fa \
-    --disable-precalc \
-    --output-dir /output \
-    --tempdir /temp \
-    --cpu 50
-```
+In case of error, using a docker container can be a solution. In this case follow the documentation of InterProScan (https://interproscan-docs.readthedocs.io/en/latest/HowToUseViaContainer.html). Make sure to have the InterProScan data which is not included in the docker image (https://interproscan-docs.readthedocs.io/en/latest/HowToUseViaContainer.html#get-interproscan-data)
+
 To remove the root files once done (here with an alpine docker image):
 ```
 docker run -it --rm -v InterProScan:/mnt:z alpine /bin/sh
 cd /mnt/
-rm -r interproscan-5.67-99.0
+rm -r interproscan-5.*
 ```