Debian-based Anduril 1.2 docker image

[Christian Frech]

Debian-based Anduril 1.2.23 docker image + Dockerfile is now publicly available at Docker Hub and GitHub, respectively.

'anduril-base' comes with the Sequencing bundle pre-installed. Further details can be found in the READMEs of both repositories.

Installation follows the semi-automatic way described at https://code.google.com/p/anduril/wiki/CloningAnduril, with some Docker-inflicted modifications (see Dockerfile).

I also plan to release my 'anduril-moksiskaan' image (version 2.05) that builds on top of 'anduril-base', but I need to clarify some licensing issues regarding contained interaction data before I can announce its availability.

The image is fully operational, except for a few component installation errors (summarized below). Not all of those errors will render the affected components dysfunctional, but some will. If component developers want help fixing these issues upstream please feel very welcome. I am happy to rebuild and push updated images once an issue has been resolved.

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Excerpts from docker build log:

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     [exec] Buildfile: /usr/local/share/anduril-bundles/sequencing/components/DiffMeth/build.xml
     [exec]
     [exec] methylKit-check:
     [exec]
     [exec] download:
     [exec]       [get] Getting: http://methylkit.googlecode.com/files/methylKit_0.5.7.tar.gz
     [exec]       [get] To: /usr/local/share/anduril-bundles/sequencing/lib/methylKit.tar.gz
     [exec]      [exec] * installing to library ‘/usr/local/lib/R/site-library’
     [exec]      [exec] ERROR: dependencies ‘GenomicRanges’, ‘IRanges’, ‘data.table’ are not available for package ‘methylKit’
     [exec]      [exec] * removing ‘/usr/local/lib/R/site-library/methylKit’
     [exec]      [exec] Result: 1

//----

     [exec] /usr/local/share/anduril-bundles/sequencing/components/GenomicRearrangement /usr/local/share/anduril-bundles/sequencing
     [...]
     [exec] Location: http://www.embl.de/~rausch/delly_v0 [following]
     [exec] --2015-05-30 09:10:05--  http://www.embl.de/~rausch/delly_v0
     [exec] Reusing existing connection to www.embl.de:80.
     [exec] HTTP request sent, awaiting response... 404 Not Found
     [exec] 2015-05-30 09:10:05 ERROR 404: Not Found.
     [exec] gzip: stdin: unexpected end of file
     [exec] tar: Child returned status 1
     [exec] tar: Error is not recoverable: exiting now
     [exec] mv: cannot stat `delly_v0.0.11/*': No such file or directory
     [exec] rm: cannot remove `delly_v0.0.11': No such file or directory

//----

Installing for components: DEE2DEG
Installing for components: ExonExpression
Installing for components: LimmaStat
[STDOUT InstallRequirements] checking mpi.h presence... no
[STDOUT InstallRequirements] checking for mpi.h... no
[STDERR InstallRequirements] configure: error: "Cannot find mpi.h header file"
[STDERR InstallRequirements] ERROR: configuration failed for package ‘Rmpi’

//----

Installing for components: GOClustering
Installing for components: GOEnrichment
Installing for components: GOProbabilityTable

[STDERR InstallRequirements] downloaded 3.5 MB
[STDERR InstallRequirements]
[STDERR InstallRequirements] ERROR: dependency ‘GO.db’ is not available for package ‘csbl.go’

//----

Installing for components: IlluminaAnnotator
[STDERR InstallRequirements] ** building package indices
[STDERR InstallRequirements] ** testing if installed package can be loaded
[STDOUT InstallRequirements] Error : .onLoad failed in loadNamespace() for 'IlluminaHumanMethylation450k.db', details:
[STDERR InstallRequirements] ERROR: loading failed
[STDOUT InstallRequirements]   call: NULL
[STDOUT InstallRequirements]   error: 'fun' is defunct.

//----

Installing for components: MeapNormalization
Installing for components: MeapQuantification
Installing for components: MeapVisualizer
Installing for components: DEE2DEG
Installing for components: ExonExpression
[STDERR InstallRequirements] ** testing if installed package can be loaded
[STDERR InstallRequirements] ERROR: dependency ‘oligo’ is not available for package ‘meap’

//----

Installing for components: FunctionalScore
[ERROR] component.xml, component FunctionalScore: Error adding test case directory /usr/local/share/anduril-bundles/sequencing/components/FunctionalScore/testcases/case1: java.io.IOException: One of 'failure' or 'expected-output' must exist; neither was found

//----

Installing bundle Sequencing
     [exec] Buildfile: /usr/local/share/anduril-bundles/sequencing/components/BICseq/build.xml
     [exec] Buildfile: /usr/local/share/anduril-bundles/sequencing/components/BismarkAlign/build.xml
         [exec] Target "setup" does not exist in the project "component-testcases".
         [exec] BUILD FAILED

//----

     [exec] Buildfile: /usr/local/share/anduril-bundles/sequencing/components/ControlFreeC/build.xml
     [exec] Buildfile: /usr/local/share/anduril-bundles/sequencing/components/Cuffcompare/build.xml
     [exec] Buildfile: /usr/local/share/anduril-bundles/sequencing/components/Cufflinks/build.xml
     [exec] Buildfile: /usr/local/share/anduril-bundles/sequencing/components/Cuffmerge/build.xml
     [exec] Buildfile: /usr/local/share/anduril-bundles/sequencing/components/DatabaseConstruction/build.xml
     [exec] Buildfile: /usr/local/share/anduril-bundles/sequencing/components/SeqQC/build.xml
     [exec] Buildfile: /usr/local/share/anduril-bundles/sequencing/components/Trimmer/build.xml
     [exec] Buildfile: /usr/local/share/anduril-bundles/sequencing/components/DatabaseQuery/build.xml
     [exec] Buildfile: /usr/local/share/anduril-bundles/sequencing/components/RegionTransformer/build.xml
     [exec] Buildfile: /usr/local/share/anduril-bundles/sequencing/components/Trimmomatic/build.xml
         [exec] Target "setup" does not exist in the project "component".
         [exec] BUILD FAILED

//----

     [exec] Buildfile: /usr/local/share/anduril-bundles/sequencing/components/Cuffdiff/build.xml
         [exec]      [exec] bash: install.sh: No such file or directory
         [exec] BUILD FAILED

//----

     [exec] /usr/local/share/anduril-bundles/sequencing/components/MethylCall/build.xml:10: The following error occurred while executing this line:
         [exec] java.io.FileNotFoundException: /usr/local/share/anduril-bundles/sequencing/components/BSAlign/build.xml (No such file or directory)

//----

     [exec] Buildfile: /usr/local/share/anduril-bundles/sequencing/components/STAR/build.xml
         [exec] /usr/local/share/anduril-bundles/sequencing/components/STAR/build.xml:11: Can't get http://csbi.ltdk.helsinki.fi/pub/anduril_static/component_data/CelllineQueryResources.RData to /usr/local/share/anduril-bundles/sequencing/components/STAR/CelllineQueryResources.RData

//----

Installing for components: AffyReader
[STDOUT InstallRequirements] Warning in .requireBiocPackage("affxparser", neededBy = pkgname) :
[STDOUT InstallRequirements]   Package 'affxparser' could not be loaded. Without it aroma.apd will not work. Please install it from Bioconductor, cf. http://www.bioconductor.org/

[Ville Rantanen]

We are working to get the installers properly working, there is an image here with sequencing bundle and requirements:

https://registry.hub.docker.com/u/anduril/sepia/

Also, there is Anduril2 image avaiable,   although that will change a lot tomorrow, when we clean up the code

[Ville Rantanen]

You should get a working sequencing bundle  (with still minor dependency problems...) with:

FROM ubuntu:14.04

RUN apt-get update && apt-get install -y wget

RUN echo deb http://anduril.org/linux/ binary/ > /etc/apt/sources.list.d/anduril.list && \

    echo deb http://cran.at.r-project.org/bin/linux/ubuntu trusty/ > /etc/apt/sources.list.d/cran-r.list && \

    wget http://anduril.org/linux/anduril_pub.gpg -O - | apt-key add -

RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 && \

    apt-get update && apt-get install -y anduril-meta anduril-local-installer && apt-get clean

RUN anduril-source-install Microarray Tools && echo "" | anduril-local-enable

RUN anduril-bundle-install Sequencing && anduril-bundle-install Anima && anduril-source-update

[Christian Frech]

Do you also have the corresponding Dockerfile online somewhere?

Please let me know once you have cleaned-up the installer, I will then re-build and upload my image.

[Ville Rantanen]

I've now included the docker file to these images' descriptions:

https://registry.hub.docker.com/u/anduril/anduril1/

https://registry.hub.docker.com/u/anduril/sepia/

The sequencing bundle has a name Sepia, because it's a part of a publication being submitted. I will most likely create another image with the "proper" sequencing bundle name, once i know the installers actually work. We have another coding session coming next week, and then i hope we have the sequencing installers done for both anduril 1.x and anduril 2.0.