Docker containers for the Regulatory Sequence Analysis Tools (RSAT)

This folder contains the installation scripts for the software suite Regulatory Sequence Analysis Tools (RSAT; http://rsat.eu/).

The installation must be executed as root user. If you are non-root but sudoer user, you can become it withn "sudo bash".

Credits

• François-Xavier Théodule
• Jacques van Helden (Jacques.van-Helden@univ-amu.fr)

The RSAT instlaler bash script was developed under Ubuntu by Jacques van Helden.

It was ported to Debian by François-Xavier Théodule, who developed the rsat_debian docker image. Jacques van Helden developed the rsat_ubuntu image with the help of Olivier Sallou.

Installation procedure

Requirements

If not done, install the latest version of docker: https://docs.docker.com/

Loading a docker image from its mount point

docker load -i  Images/rsat_debian-2016-07-15.tar.gz

Checking the available docker images

docker images

Example of result:

REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE
rsat-commands       2016-10-26          7055c53a521e        46 hours ago        4.543 GB
ubuntu              16.04               f753707788c5        2 weeks ago         127.2 MB
rsat_debian         2016-07-13          5021cd9759f6        3 months ago        1.804 GB
debian              jessie              1b088884749b        4 months ago        125.1 MB
rsat_debian         2016-07-13.prepa    1b088884749b        4 months ago        125.1 MB

Start a container with the RSAT Web server

The following command sarts a container with an RSAT Web server visible at port 32801 of the local host. The server has 1Gb RAM, and a mount point to a shared space folder on /rsat_data.

mkdir -p ~/rsat_data

docker run -t -i -m 1g  -v ~/rsat_data:/rsat_data -p 32801:80 rsat_debian:2016-07-15

The RSAT server can then be accessed from a Web browser, at URL http://[host.ip.address]/:32801/rsat.

If you are working directly on the host machine, the server should be visible at http://localhost:32801/rsat. If you are connected remotely, you need to know the external IP address of the host machine. ¹

Note that the Web server remains active in the active container, but is stopped when exiting this container.

Running an RSAT command on the docker container since the host machine

executer une commande rsat depuis sa machine physique (volume partage entre conteneur et machine physique /RsatInstall et /tmp) via un conteneur

Ajouter en fin de ligne precedente( "docker run" ) la commande rsat a executer, ses parametres , fichiers d'entree et un emplacement de sortie de resultat . A noter que dans ce cas le conteneur se referme automatiquement après execution de la commande

Exemple : commande rsat /rsat/perl-scripts/retrieve-seq Parametres -org Saccharomyces_cerevisiae -feattype gene -type upstream -format fasta -label name -from -800 -to -1 Fichier d'entree de la commande rsat : /RsatInstall/list.genes (vu depuis le conteneur ou /tmp/list.genes vu depuis l'hote hebergeur) Fichier de sortie /tmp/output sur l'hote

docker run -t -i -m 1g -v /tmp:/RsatInstall -p 32801:80 rsat_debian:3.1.0 /rsat/perl-scripts/retrieve-seq -org Saccharomyces_cerevisiae -feattype gene -type upstream -format fasta -label name -from -800 -to -1 -i /RsatInstall/list.genes > /tmp/output

Avec un fichier d'entrée :

more /tmp/list.genes 
DAL5
GAP1
MEP1
MEP2
PUT4
MEP3
DAL80

On a un fichier de sortie /tmp/output

root@Theodule-VBox-Clone:/home/tagc# more  /tmp/output
>DAL5   DAL5; upstream from -800 to -1; size: 800; feature type:gene; location: Saccharomyces_cerevisiae:NC_001142.7:718860:719659:D
GAACATCTGTTTAACTTTCAAGCTTTCTACCATATAGCCGAGATGAGCAAATACATTAAA
ACATCAAAAAGTGGTGCTTGAATGCTTATTTTATGACGCAAAGCAGATGTAATGCATCCC
GAGTAAAACAGAATACTTAATTTGACTTCAGCAAAATAACTACCCAGAATGAACACCGAA
TTTGACATTGATAACAAGACAATCTAGGAATACTTTTACATCAGCACAATATCCATGGTG
GATCCCGGCGGATTTTTCTTTCTTATTGCACCTTAATCAGGTTTACAGCCTATGACTGAC
TCTGGAGTGTCCTTTCCCAGTATCTGATTGTTTCCGCAACATCTATGCATATCAGAGAAG
CGTTCTCATCAGTCACTTGACAAATGCTCGAGGAGCTATCATTTGCTGATAAGGTGCTAC
AGCGCGCTCCTGCCGCACGCTTTGTTCCTTTTCGATAAGAGTCCCTCGCGTTAGTCTGAG
TGAAGTGCGGAATTCAGCAAACGAATAACAATCGACCTTATGATCATGTGGATTATCGGG
GCAAAAGATTTGGCCAAGATGTCAGAGAACGTTATCACCAATCACTCACACAATTAAGTG
GTAGTGTAACTCCGAAGATACGGCTAATACTTATCATTATCTGGTTTTCCGAATATACAG
ATTGGATGAAGTAATATATGTATATAAATGGACCAAGGAAACATCAAATTAGGAGATCAT
GAGGGAAAGGTTTAACATAACAACATTGAAGAAAACAACAAAACAAGGATAATCAAATAG
TGTAAAAAAAAAAATTCAAG
>GAP1   GAP1; upstream from -800 to -1; size: 800; feature type:gene; location: Saccharomyces_cerevisiae:NC_001143.7:513905:514704:D
CCTACAACAATAGATTAGACACACCAGTGCCAAGGACAATATGTTGCGTTCTGACTAGTC
GAAGTATCATTACGCTGTGCAGATCGACCTGACACCAGACACAAAGGAGAATAGGGGCAG
CATGAGTTCCGTCGGCGACTCATTCCGACCTTCCACAGGTCCGTTGATTACTTTTTCACT
GATCCGGTGGAATCTATGGTTGTTTTTTTCATCATGATATCTGTTTTAGGACTTTTTTTT
TCAGCCGATCGCTTATCTGCTCACTAGAATCGTAATCAGTGATATTTTTATTAATAATTA
TTATTTATTTTTTTTTATACCATTTCCTTTTGATAAGGGGTCGTTGGTGCCGTGCCGCTA
TCAGGCAGCCTCACTAATCTACCCATTGACCTCATGCAGCAAAGTCACATCGCCCATATC
TCTCGAGTGCGATAACGGGGAACTTGATTTGGTAACTGATAAGATTGTTAAATGTCAGTT
TGGATGCTTTTTCTTACGTCCGATTAGCTTATCTTCTGGAGCAACCGGCCATTTACCTCC
TCATAGTAAATTAAACATGATAAGCGCATAGTTGGGGCAACACACCTTTCTTCCGGAATT
CGCTCTGGATGAGACATATAAAGATGAAGGTGAAGTCCACTTAAATGAATGTCAATGAGA
CGATGTTTTTTCTCCTAGATTGATTTTTGAATTCCTTGTATACAAAGTCTTGTTTTCTTA
TTGTCCTCAACAAAACAAAAGTAGAAAAGAACAGACCAAGGACAGCAACATTTATAAGAA
ACAAAAAAAAGAAATAAAAA
>MEP1   MEP1; upstream from -800 to -1; size: 800; feature type:gene; location: Saccharomyces_cerevisiae:NC_001139.8:732933:733732:R
AGAGCTATTTGTAAGGGAAGACAAGATCTCAAGTGTTACCACAGCCCGTAATTGAGTTCG
GCACTATTCGAGCGCACAAAAAATCCCGTACTGTTTTTTTTCAGATAAGAAAGACTGAGC
CTATATAAACACTACCTGAACCATTTTTAAGATAAAAGTTATATACGATAGAGTTATCCC
CTCTTAATAATTGATCAAGAACCTCTGAAGCACAAAAGGGAGCATAAGAGCACTTAGGGA
CAAACGTATTTCTTTCCCCCACTCCCCTTTTTCCCTTTGCGATGCACATCCATAACTTGT
ACTTGTGTCTTGACATTCTTCAAAATCAACATGGCGATGCTCTTCTACGGTTGTCCTTTG
CCACGAACTTTGTTTTGCGCCTCCCCTCCCTTTGTCAGGCTGAGTGCAAAAGAAAAGGCC
CTGGTTGCTTATCTCTGCGGACACGCGCCCCTCTTATTGGATGAGACATCTCAGAGATTG
CGATAACGATAAGATTCACAATTGCTACAGACACCCTTGTGTGACATCTTATGGCTATGT
AAGCACAGAAGAGAAGAAGAAAGAAATGACAAAGTATTGATGGAAGATGTTTTTCCTGAA
AAAAAAAAAAAAAAAAAATCGGAAAAGTGGTGTAGGCTTCTATAGCACCTTCTGCTTACC
AGTCGATAATGCAGTTCCAGAATAAGATACTTAAAAGGTAGTTTATTTATATAGGCGCTC
TTGTAACTTGTTTAGGCTTATGATCAGAGAATTATTTTAGTAAACATAACTGCAGTACGG
ATTCTTATACTGTAGAAACT
>MEP2   MEP2; upstream from -800 to -1; size: 800; feature type:gene; location: Saccharomyces_cerevisiae:NC_001146.6:356655:357454:D
TGAGTTTTCTTTTTCTGATATTATTGGATAATATTTTCAGCTATAGACTATCATCATTCA
GCATTGGTCACGCTAAAATATACGTTCCATGCATACGTGATAGCCTACTCGGTTGTCAAC
TTCATTTTATAGGCTGCCTGGTCACCGATTACCGCCCCGCTCAGCAGGACGGTTTAAGCT
TCTGTTCTTGGAAACGACGTAATTCATGTCGGCCATCGAAATCATTCCTGGCTTTGTAAT
AGTCATAATGAACAAGGAATGCTGTCTTGGGTTTTTTTCCCTTTGCGAATACCCGGGCTG
CCAAAATAGAAAAGGAACAAATGGTAGGTCTTTAAGATAAGAAAGATAAGATAAGACATC
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCGATAACAAAGAAGAATCCTTCGGTCT
CTTCTTACTGCTGTTACTGCTTATCAAGAGTGTCTGGTAATAGTCAAAGCCAGATAAGAT
AAGAAATGTAAAATCGACTATTTCCCTCGTAAAAAGCTTCAATTGCTCACGCATCGACGA
ATACTAAGCGGCGTGAAGACCCTGTGCCTTATCAATGAAGTATTCAGTACAAGAGGTGTT
CATTCCGAGCCACTTTTCTGCACCATATATAAGCAGTAGTTACACATGTGCTAACCAAAC
ATCAGTGGGTAGTAATCATTCGTGCTTTCACGTCCTTTCAAATTAAATATCCTTCTTAAA
TAATAAGTCTGCACAGAGCTTTGAAAGAAGTTTAGTTTTGTAATATATCATACTTAATAT
ATTACAATACAATATCAACA
>PUT4   PUT4; upstream from -800 to -1; size: 800; feature type:gene; location: Saccharomyces_cerevisiae:NC_001147.5:988780:989579:R
TCTAAAACGGAGATCAAATACCGGGCCCGCGCGCGATGGCCGGATGTCCGTCCATACTGC
AATGTGAATTCCCGCGCGGTTCAAATCTTGTCACAAGTTTGTCAAAATTGCTTGTCATGT
CTGCCAAATCTCCAGGGTCCTAAATCTGAGGTAGCACGGCACGGCACAAGATGGTACCCA
TGGTGCGTGACGACAGCCGCTACTTGCACGGCTTTGTTCCGGCAGCCCGGGTACCCGCGC
TGCGAGTTGAAACATCATCAAACCAAAAGGGAAGCGACGTTAGTTTTTTTCATTGCGCTA
GCTATGACGTTTGGGTGGCCTAGCCGGTTCGCGTGTGCCTGTCGCTTTTGTCGCTTTTCA
ACTTCTGCCCGATATTTCCTATCAAAGGAAAATGGGACGTTTTCAACCCCTCGCTATCAT
CGTGCCTGCACTCTGCCTATCGCCAACTACACCGGGGTTTTATCTGCTTCACCCCTCCAT
CCAGTGCTGATAACAAGAAGAACCTTGCAGGGTAGGGCAGGACCTACGGCCAAAATACTA
ATTATGTCTGTTTATGTACATGCCCCAATCTGAATATTCCATGAATGTAGGCACAGCATA
TCTCCATCCATGTACTGATACAGACGCATAAACATATATGTATATACATACTTATACACT
CGAATATTTGTAGACTGATGTACTTCTATATATATATAGGGGGTTTGTGTTCCTCTTCCT
TTCCTTTTTTTTTCTCTCTTCCCTTCCAGTTTCTTTTATTCTTTGCTGTTTCGAAGAATC
ACACCATCAATGAATAAATC
>MEP3   MEP3; upstream from -800 to -1; size: 800; feature type:gene; location: Saccharomyces_cerevisiae:NC_001148.3:812450:813249:R
GCGACAAATATAAACTAGTCTCACGGAAGTTAGATGTTGAATCTAAGAGGAATTTTGTGA
AGGAATATATCAGCGATCAACGTAAAAAGAGGAAGTAGAAATACTTATGAAGGCATGCAT
GCATGCATACATATTTATATATATATGTCTTTAGGAGTATGTATTGCATTTAATCGAAAC
AAACAAGAAAAAGAAGAGTAGATGTGCCCGTTTCTGTCACTCCTATTTACTGACACTTTC
TTGACCTACCTCAAACCAGTTCCAGTTCCGGCAAAAAGTGCCGCGCGGCGGAGAAACATC
TCCACCTTATCTCGGCGCCAAATCCTTATCTCTCGTAGCTGGTTTGCCCGCGATAAGGCG
GGCGAGTTATTTTGAAGTTTTCCATAAACTGGTTTTCCATCTCGAGGTTTTTCCTCGCTT
TCCACGCTATGACCCTTTTTAGTTAAGGTACCCGATGGCATACTTTATATATTATATATA
TATGTTAAGTTAATATGTTTTAGCAGATTTGATATGCTGATATGCAGCACGGACTTTCCC
TCTCCTTGTCTTATCGCATCTTATCGCAACAATTTGATAGATATCTTCTCCCTTTCCTAT
CTTGTAGAATAAGGTTGTGTGCTTTGAGTCTGATAGCCGTCTTCTTTCGGTCGCTTCTTC
TCTCTTTTGGTTCTTTGATTGTCTATTACAATCAATGCAGGCTAGTTAAGGGTCCAATCA
CTTTTGAAATTGTTTTGTAAAAAGCGAAGGCATTTTTTTTTTAGAAGATACAATTGAAAA
CATATAGATTTAGAGTTCAC
>DAL80  DAL80; upstream from -800 to -1; size: 800; feature type:gene; location: Saccharomyces_cerevisiae:NC_001143.7:505740:506539:D
GTTCATTAGAGTGCATAATATGGTCTAATGAGTGGTTCGGTGACACATCACTCAGGTTTC
TATCTACAAAGGATTTGGGCAATGCATGCTTCCTCTCCGCCTCCTTGCCGTTGGGAGTTC
TTCGTTTTTCTCTTTGTAAACTGCTAGTCAGATTGCCATTCTCAGGTAATTGCCGCAATA
CTTCTTGGTTTTCTAACTCATCTGGTCTCGAATTTACTCTATCTACTTCTTCAGTCACCG
ATCTATCTGCCTGAGGTGGAGCGAAGTGAGTTCCAGACGCTGTTGACACGTTAGACATCA
CCCTTGTTTATCTATCCTACCTTTTCTTCTTGCGTACGTGCCTCTCAATGCGTCGTGTGA
ATTATCAGTGACCGGTCGTGCCTATAATGTCCTGCTAATTTCCCACTAAATCTTTCCCCA
TGGCGTATTCATCGTTATGTTTGTGTCTTTTGTTCAACCCAAAGGGCTGTAGCAATCTTC
ACCCGTTTGTCGTTGATAACGAGTTTCCACCTTATCACTTATCACTAGTGCTAATCAAAC
AGCAAAGAATGCTTGATAGAAACCGATCCTGGGCTTATCTCGCTGCATTGTGGCGGCATC
CCTGGACTGTAATCAGCAAGTGTTGCTTAGTATATATATACATCCAGCGTCAGCTTGAAT
TTGGATACAGTTACTGTTTTTTCGATTTTCTCTTGGTTATTCTTTCTGAGACAGTAGTAA
TTTTGTATTACTGAGCGGGATATTGTTTATCTGCCGTCATACTATATTACATTATATTAT
ATCATATTATATATAAGAGA

Running a docker on the command line

mkdir -p ~/Docker

docker run -t -i -m 1g  \
    -v  ~/Docker:/DockerIn \
    -v ~/Docker:/DockerOut \
    -v ~/Docker:/DockerTodo \
    rsat_debian:2016-07-13 /no_backup/RSAT_Docker/DockerTodo.sh \
    > ~/Docker/output.txt