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./biodocker/Dockerfile

  • Version: 1
  • Software: BioDocker base Image
  • Software Version: 20150814
  • Base Image: scratch
  • Build Cmd: docker build --rm -t biodckr/biodocker .
  • Pull Cmd: docker pull biodckr/biodocker
  • Run Cmd: docker run --rm biodckr/biodocker bash

./BLAST/2.2.28-2/Dockerfile

  • Version: 1
  • Software: NCBI BLAST+
  • Software Version: 2.2.28-2
  • Description: basic local alignment search tool
  • Website: http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download
  • Tags: Genomics|Protemomics|Transcriptomics|General
  • Provides: blast 2.2.28-2
  • Base Image: biodckr/biodocker:latest
  • Build Cmd: docker build --rm -t biodckr/ncbi-blast 2.2.28-2/.
  • Pull Cmd: docker pull biodckr/ncbi-blast
  • Run Cmd: docker run --rm biodckr/ncbi-blast

./Clustal-Omega/1.2.1-1/Dockerfile

  • Version: 1
  • Software: Clustal-omega
  • Software Version: 1.2.1-1
  • Description: general purpose multiple sequence alignment program for proteins
  • Website: (http://www.clustal.org/omega/
  • Tags: Proteomics
  • Provides: Clustal-omega 1.2.1-1
  • Base Image: biodocker:latest
  • Build Cmd: docker build --rm -t biodckr/clustalo 1.2.1-1/.
  • Pull Cmd: docker pull biodckr/clustalo
  • Run Cmd: docker run --rm biodckr/clustalo

./Comet/2015011/Dockerfile

  • Version: 1
  • Software: Comet
  • Software Version: 2015011
  • Base Image: biodckr/biodocker:latest
  • Build Cmd: docker build -t biodckr/comet 2015011/.
  • Pull Cmd: docker pull biodckr/comet
  • Run Cmd: docker run biodckr/comet

./Comet/2015012/Dockerfile

  • Version: 1
  • Software: Comet
  • Software Version: 2015012
  • Base Image: biodckr/biodocker:latest
  • Build Cmd: docker build -t biodckr/comet 2015012/.
  • Pull Cmd: docker pull biodckr/comet
  • Run Cmd: docker run biodckr/comet

./Comet/2015020/Dockerfile

  • Version: 1
  • Software: Comet
  • Software Version: 2015020
  • Description: basic local alignment search tool
  • Website: http://comet-ms.sourceforge.net/
  • Tags: Proteomics
  • Provides: Comet 2015020
  • Base Image: biodckr/biodocker:latest
  • Build Cmd: docker build --rm -t biodckr/comet 2015020/.
  • Pull Cmd: docker pull biodckr/comet
  • Run Cmd: docker run --rm biodckr/comet

./Crux/2.1/Dockerfile

  • Version: 1
  • Software: Crux
  • Software Version: 2.1
  • Description: a software toolkit for tandem mass spectrometry analysis
  • Website: http://cruxtoolkit.sourceforge.net/
  • Tags: Proteomics
  • Provides: crux 2.1
  • Base Image: biodckr/biodocker:latest
  • Build Cmd: docker build --rm -t biodckr/crux 2.1/.
  • Pull Cmd: docker pull biodckr/crux
  • Run Cmd: docker run --rm biodckr/crux [./crux ./xlink-assign-ions ./xlink-score-spectrum]

./denovoGUI/1.5.2/Dockerfile

  • Version: 1
  • Software: denovogui
  • Software Version: 1.5.2
  • Description: graphical user interface for de novo sequencing of tandem mass spectra
  • Website: https://code.google.com/p/denovogui/
  • Tags: Proteomics
  • Provides: denovogui 1.5.2
  • Base Image: biodckr/biodocker:latest
  • Build Cmd: docker build --rm -t biodckr/denovogui 1.5.2/.
  • Pull Cmd: docker pull biodckr/denovogui
  • Run Cmd: docker run --rm -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix biodckr/denovogui

./DIA-Umpire/1.4256/Dockerfile

  • Version: 1
  • Software: DIA-Umpire
  • Software Version: 1.4256
  • Description: computational analysis of data independent acquisition (DIA) mass spectrometry-based proteomics data
  • Website: http://diaumpire.sourceforge.net
  • Tags: Proteomics
  • Provides: dia-umpire 1.4256
  • Base Image: biodocker:latest
  • Build Cmd: docker build --rm -t biodckr/diaumpire 1.4256/.
  • Pull Cmd: docker pull biodckr/diaumpire
  • Run Cmd: docker run --rm biodckr/diaumpire

./EMBOSS/6.6.0-1/Dockerfile

  • Version: 1
  • Software: emboss
  • Software Version: 6.6.0-1
  • Description: software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community
  • Website: http://emboss.sourceforge.net/what/
  • Tags: Proteomics|Genomics|General
  • Provides: emboss 6.6.0-1
  • Base Image: biodckr/biodocker:latest
  • Build Cmd: docker build --rm -t biodckr/emboss 6.6.0-1/.
  • Pull Cmd: docker pull biodckr/emboss
  • Run Cmd: docker run --rm biodckr/emboss

./MSAmanda/1.0.0.5242/Dockerfile

  • Version: 1
  • Software: MSAmanda
  • Software Version: 1.0.0.5242
  • Description: scoring system to identify peptides out of tandem mass spectrometry
  • Website: http://ms.imp.ac.at/?goto=msamanda
  • Tags: Proteomics
  • Provides: MSAmanda 1.0.0.5242
  • Base Image: biodckr/biodocker:latest
  • Build Cmd: docker build --rm -t biodckr/msamanda 1.0.0.5242/.
  • Pull Cmd: docker pull biodckr/msamanda
  • Run Cmd: docker run --rm biodckr/msamanda

./MSGFp/9949/Dockerfile

  • Version: 1
  • Software: MSGF+
  • Software Version: 9949
  • Description: MS/MS database search tool
  • Website: http://proteomics.ucsd.edu/Software/MSGFPlus/
  • Tags: Proteomics
  • Provides: MSGFPlus 9949
  • Base Image: biodckr/biodocker:latest
  • Build Cmd: docker build --rm -t biodckr/msgfp 9949/.
  • Pull Cmd: docker pull biodckr/msgfp
  • Run Cmd: docker run --rm biodckr/msgfp

./Novor/1b/Dockerfile

  • Version: 1
  • Software: Novor
  • Software Version: 1b
  • Description: real-time peptide de novo sequencing
  • Website: http://www.rapidnovor.com/
  • Tags: Proteomics
  • Provides: novor 1b
  • Base Image: biodckr/biodocker:latest
  • Build Cmd: docker build --rm -t biodckr/novor 1b/.
  • Pull Cmd: docker pull biodckr/novor
  • Run Cmd: docker run --rm biodckr/novor

./OpenMS/1.11.1-3/Dockerfile

  • Version: 1
  • Software: OpenMS
  • Software Version: 1.11.1-3
  • Description: C++ libraries ans tools for MS/MS data analysis
  • Website: http://open-ms.sourceforge.net/
  • Tags: Proteomics
  • Provides: openms 1.11.1-3
  • Base Image: biodckr/biodocker:latest
  • Build Cmd: docker build --rm -t biodckr/openms 1.11.1-3/.
  • Pull Cmd: docker pull biodckr/openms
  • Run Cmd: docker run --rm biodckr/openms

./PepNovo+/20120423/Dockerfile

  • Version: 1
  • Software: PepNovo+
  • Software Version: 20120423
  • Description: de novo sequencing of low precision MS/MS data
  • Website: http://proteomics.ucsd.edu/Software/PepNovo/
  • Tags: Proteomics
  • Provides: PepNov+ 20120423|dos2unix
  • Base Image: biodckr/biodocker:latest
  • Build Cmd: docker build --rm -t biodckr/pepnovo 20120423/.
  • Pull Cmd: docker pull biodckr/pepnovo
  • Run Cmd: docker run --rm biodckr/pepnovo

./Rstudio-Proteomics/Dockerfile

  • Version: 1
  • Software: Rstudio
  • Software Version: ?
  • Description: Rstudio-Proteomics is an adaptation from the original images provided by the Rocker-org. The container provided here contains a Rstudio server configurated with several packages dedicated to Proteomcis data analysis.Rstudio-Proteomics is an adaptation from the original images provided by the Rocker-org. The container provided here contains a Rstudio server configurated with several packages dedicated to Proteomcis data analysis.
  • Website: https://github.com/rocker-org
  • Tags: Genomics|Proteomics|Transcriptomics|Metabolomics|General
  • Provides: Rstudio
  • Base Image: bioconductor/release_core
  • Build Cmd: docker build --rm -t biodckr/rstudio .
  • Pull Cmd: docker pull biodckr/rstudio
  • Run Cmd: docker run --rm -p 8787:8787 biodckr/rstudio
  • Extra: The Rstudio will be available via browser at:
  • Extra: http://localhost:8787
  • Extra: user: rstudio
  • Extra: pass: rstudio

./SearchGUI/1.30.1/Dockerfile

  • Version: 1
  • Software: SearchGUI
  • Software Version: 1.30.1
  • Description: graphical user interface for proteomics identification search engines
  • Website: https://code.google.com/p/searchgui/
  • Tags: Proteomics
  • Provides: searchgui 1.30.1
  • Base Image: biodckr/biodocker:latest
  • Build Cmd: docker build --rm -t biodckr/searchgui 1.30.1/.
  • Pull Cmd: docker pull biodckr/searchgui
  • Run Cmd: docker run --rm biodckr/searchgui

./Tandem/10-12-01-1/Dockerfile

  • Version: 1
  • Software: X!Tandem
  • Software Version: 10-12-01-1
  • Description: software that can match tandem mass spectra with peptide sequences
  • Website: http://www.thegpm.org/tandem/
  • Tags: Proteomics
  • Provides: tandem 10-12-01-1
  • Base Image: biodckr/biodocker:latest
  • Build Cmd: docker build --rm -t biodckr/tandem 10-12-01-1/.
  • Pull Cmd: docker pull biodckr/tandem
  • Run Cmd: docker run --rm biodckr/tandem

./TOPPAS/1.11.1-3/Dockerfile

  • Version: 1
  • Software: OpenMS
  • Software Version: 1.11.1-3
  • Description: a graphical workflow editor for the analysis of high-throughput proteomics data
  • Website: http://open-ms.sourceforge.net/workflow-integration/toppasworkflows/
  • Tags: Proteomics
  • Provides: openms 1.11.1-3|topp 1.11.1-3
  • Base Image: biodckr/biodocker:latest
  • Build Cmd: docker build --rm -t biodckr/toppas 1.11.1-3/.
  • Pull Cmd: docker pull biodckr/toppas
  • Run Cmd: docker run --rm -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix biodckr/toppas

./TPP/4.8/Dockerfile

  • Version: 1
  • Software: TPP
  • Software Version: 4.8
  • Description: a collection of integrated tools for MS/MS proteomics
  • Website: http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP
  • Tags: Proteomics
  • Provides: tpp 4.8.0
  • Base Image: biodckr/biodocker:latest
  • Build Cmd: docker build --rm -t biodckr/tpp 4.8/.
  • Pull Cmd: docker pull biodckr/tpp
  • Run Cmd: docker run --rm biodckr/tpp
  • Extra: This container only posses the binary files, the web interface is not configurated