@bgruening I have try to download a container is quay.io using rkt and I'm receiving the following error:

rkt fetch --no-store quay.io/biocontainers/bedtools
image: searching for app image quay.io/biocontainers/bedtools
image: remote fetching from URL "https://quay.io/c1/aci/quay.io/biocontainers/bedtools/latest/aci/linux/amd64/"
image: keys already exist for prefix "quay.io/biocontainers/bedtools", not fetching again
image: downloading signature from https://quay.io/c1/aci/quay.io/biocontainers/bedtools/latest/aci.asc/linux/amd64/
fetch: bad HTTP status code: 404

From @sauloal on September 24, 2015 14:45

https://github.com/jfass/compass

Copied from original issue: BioContainers/sandbox#38

From @sauloal on September 24, 2015 14:45

http://korflab.ucdavis.edu/datasets/cegma/

Copied from original issue: BioContainers/sandbox#39

https://www.broadinstitute.org/gatk/

From @sauloal on September 23, 2015 20:6

http://cnsgenomics.com/software/gcta/

Copied from original issue: BioContainers/sandbox#5

Hi.
I have some problem with run containter:
$ docker run -v /root/test/:/data/ samtools '/usr/local/bin/samtools view -F 4 -Sb /data/tuberculosis.sam > /data/tuberculosis.bam'

I got errors:

exec: "/usr/local/bin/samtools view -F 4 -Sb /data/tuberculosis.sam > /data/tuberculosis.bam": stat /usr/local/bin/samtools view -F 4 -Sb /data/tuberculosis.sam > /data/tuberculosis.bam: no such file or directory
Error response from daemon: Cannot start container b63e8e4b2cffe04579b5d7caff8a8a71ff9eb3627f7b9b03ad076ae250c98b4d: [8] System error: exec: "/usr/local/bin/samtools view -F 4 -Sb /data/tuberculosis.sam > /data/tuberculosis.bam": stat /usr/local/bin/samtools view -F 4 -Sb /data/tuberculosis.sam > /data/tuberculosis.bam: no such file or directory

Can you, please, explain what am u doing wrong?
But when i run simple samtools it's work fine:
$ docker run -v /root/test/:/data/ samtools '/usr/local/bin/samtools

Program: samtools (Tools for alignments in the SAM format)
Version: 1.2 (using htslib 1.2.1)

Usage:   samtools <command> [options]

Commands:
  -- indexing
         faidx       index/extract FASTA
         index       index alignment
  -- editing
         calmd       recalculate MD/NM tags and '=' bases
         fixmate     fix mate information
         reheader    replace BAM header
         rmdup       remove PCR duplicates
         targetcut   cut fosmid regions (for fosmid pool only)
  -- file operations
         bamshuf     shuffle and group alignments by name
         cat         concatenate BAMs
         merge       merge sorted alignments
         mpileup     multi-way pileup
         sort        sort alignment file
         split       splits a file by read group
         bam2fq      converts a BAM to a FASTQ
  -- stats
         bedcov      read depth per BED region
         depth       compute the depth
         flagstat    simple stats
         idxstats    BAM index stats
         phase       phase heterozygotes
         stats       generate stats (former bamcheck)
  -- viewing
         flags       explain BAM flags
         tview       text alignment viewer
         view        SAM<->BAM<->CRAM conversion

From @sauloal on September 24, 2015 14:52

http://www.cbcb.umd.edu/software/quake/

Copied from original issue: BioContainers/sandbox#47

@BioDocker/contributors @lgatto We should arrive to a conclusion with the R packages. Please take the time to think about how we can move forward this. For the R package we want to following use cases:

• contain the bioconductor ready to use.
• contain other packages that are not included in Bioconductor and are interested for the community.
• Examples about How to used.

From @sauloal on September 24, 2015 13:44

http://cseweb.ucsd.edu/~ppevzner/software.html#EULER-short
http://euler-assembler.ucsd.edu/

Copied from original issue: BioContainers/sandbox#28

I came accross today a container on dockerhub (this one is not present in the registry UI) which doesn't seem to have any tags available nor being pushed:

https://hub.docker.com/r/biocontainers/openms/

On this one builds failed apparently. But I guess we probably want to clean up those from docker hub to avoid users being discouraged by thinking that the containers are not working/not available. This was also under biodckr user on dockerhub as well I think. You probably want to get rid of that user, or of its containers.

Hi, on BioDocker there is currently a containter for "biodckr/bowtie" (v.1.1.2)(https://hub.docker.com/r/biodckr/bowtie/). Are there plans to create a container for bowtie2 (v.2.2.9)(http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)? Bowtie and bowtie2 are really two separate applications; it would be very helpful to have a container for bowtie2.

The Gitter badge in your readme points to https://gitter.im/BioDocker/biodocker, but I think it should point to https://gitter.im/biocontainers/Lobby or https://gitter.im/biocontainers/containers?

Posted this in the 'bioconda-recipes' repo earlier and was directed here. I'm trying to build a Docker image with the variant-effect-predictor package and another tool, but I'm running into an issue with the installed script not detecting the required CGI Perl module.

I'm using the base image from BioContainers to manually test the VEP install. The installation with conda seems to work fine, but I get an error when I try to run the tool. It seems to be looking in the default Perl path for the container but not the conda-specific path. I can't tell whether this is a problem with the BioContainers image or with the VEP recipe.

Dockerfile here: https://github.com/BioContainers/containers/blob/master/biocontainers/Dockerfile

docker run -it biocontainers/biocontainers:latest

biodocker@0d70df106dd3:/data$ conda install variant-effect-predictor=86

Here's the error message:

biodocker@0d70df106dd3:/data$ variant_effect_predictor.pl --help
Can't locate CGI.pm in @INC (you may need to install the CGI module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at /opt/conda/bin/variant_effect_predictor.pl line 46.
BEGIN failed--compilation aborted at /opt/conda/bin/variant_effect_predictor.pl line 46.

Confirming that CGI was installed by the conda recipe under /opt/conda/lib/:

biodocker@0d70df106dd3:/data$ ls /opt/conda/lib/perl5/site_perl/5.22.0/
Algorithm  CGI.pod  Encode     HTML  LWP.pm      Sub     WWW       lwpcook.pod
Archive    Capture  Exception  HTTP  Mozilla     Test    YAML      lwptut.pod
Bio        Class    Exporter   IO    Net         Text    YAML.pm   x86_64-linux-thread-multi
CGI        Data     Fh.pm      IPC   SUPER.pm    URI     YAML.pod
CGI.pm     Devel    File       LWP   Statistics  URI.pm  auto

@BioDocker/contributors, Docker allows us to use the LABELS command to add metadata to images. This can be used in searched via docker client and it can aso be used by the API.

You can read more about it here.

So, my question here is; Should we add this command to the metadata we already have in our Dockerfiles ? What do you think?

i'm running the following command
~/Softwares/bismark/bismark -n 1 --path_to_bowtie ~/Softwares/bowtie2 --samtools_path ~/Softwares/samtools ~/Softwares/rat_genome/rn5 ~/Softwares/trim_galore/C8Y92ACXX.sequence.fastq

and i'm getting all the time this error:
(ERR): bowtie2-align exited with value 141

From @sauloal on September 24, 2015 14:55

http://gage.cbcb.umd.edu/recipes/msrca.html

Copied from original issue: BioContainers/sandbox#50

From @sauloal on September 24, 2015 14:51

http://denovoassembler.sourceforge.net/publications.html

Copied from original issue: BioContainers/sandbox#46

From @sauloal on September 24, 2015 14:48

http://repeatmasker.org/RMDownload.html

Copied from original issue: BioContainers/sandbox#41

From @sauloal on September 24, 2015 14:54

http://www.cbcb.umd.edu/software/bambus

Copied from original issue: BioContainers/sandbox#48

From @sauloal on September 24, 2015 13:52

Recognising Errors in Assemblies using Paired Reads
https://www.sanger.ac.uk/resources/software/reapr/

Copied from original issue: BioContainers/sandbox#36

From @sauloal on September 24, 2015 13:50

http://omictools.com/gam-ngs-s10382.html

Copied from original issue: BioContainers/sandbox#33

Hi @BioDocker/contributors

Since we are moving to a Conda/BioConda management system for our binaries, I want to clean the base image. Currently, our base image has 1.036 GB, so that means its pretty bloated. How can we start doing that? should we clean the apt-get command and then fix the ones that break? Suggestions are welcome.

Trying to execute:

docker pull quay.io/biocontainers/openbabel

gives

Using default tag: latest
Pulling repository quay.io/biocontainers/openbabel
Tag latest not found in repository quay.io/biocontainers/openbabel

However, the registry-ui recommends to pull with that command, see container pull command here.

From @sauloal on September 24, 2015 14:51

https://github.com/vice87/gam-ngs

Copied from original issue: BioContainers/sandbox#45

From @sauloal on September 24, 2015 14:46

http://busco.ezlab.org/

Copied from original issue: BioContainers/sandbox#40

From @sauloal on September 24, 2015 14:49

https://github.com/ucdavis-bioinformatics/qrqc

Copied from original issue: BioContainers/sandbox#44

Hi everyone, I'm working in two containers, one is about GROMACS and other is about GAMESS. This containers are interesting to the project?

From @sauloal on September 24, 2015 14:49

https://github.com/ucdavis-bioinformatics/scythe

Copied from original issue: BioContainers/sandbox#43

Is it possible to update biodocker to the latest LTS or maybe keep the old and a latest container to build containers with updated software ?

From @sauloal on September 24, 2015 14:57

http://sourceforge.net/projects/telescoper/

Copied from original issue: BioContainers/sandbox#52

Hi,

Is sudo not available in biocontainers for some reason? Am I not supposed to use this base container to install stuff (not via a dockerfile) interactively?

Why I want this: I'm running a biocontainers container (pulled the image few moments ago) with the following command:

docker run -it biocontainers/biocontainers /bin/bash

once inside I'm trying to install something with apt-get. This is part of an introduction to Computational Biology were I would like to explicitly teach my students how to install stuff with things like apt-get install and make.

When I try:

apt-get update I get the expected Permission denied. However, if I try with sudo:

sudo apt-get update
bash: sudo: command not found

Am I missing something? Maybe the way I run the container´?. I could be doing this in the ubuntu image but I wanted to use the biocontainers because it has already installed some useful stuff, like curl and wget.

From @sauloal on September 24, 2015 14:45

http://korflab.ucdavis.edu/datasets/cegma/

Copied from original issue: BioContainers/sandbox#39

From @sauloal on September 24, 2015 14:54

http://www.cbcb.umd.edu/software/bambus

Copied from original issue: BioContainers/sandbox#48

From @sauloal on September 24, 2015 19:30

https://github.com/jstjohn/SimSeq

Copied from original issue: BioContainers/sandbox#53

From @sauloal on September 24, 2015 14:56

http://cnag.bsc.es/

Copied from original issue: BioContainers/sandbox#51

From @edeutsch on January 20, 2017 5:3

Hi, I see that you have the Trans-Proteomic Pipeline (TPP) as a container, but it is an older version 4.8. There is now a 5.0 version of TPP out. Can we get new TPP 5.0 containers available? How can we help?

thanks,
Eric

Copied from original issue: BioContainers/sandbox#74

From @sauloal on September 24, 2015 14:49

https://github.com/ucdavis-bioinformatics/qrqc

Copied from original issue: BioContainers/sandbox#44

From @sauloal on September 24, 2015 13:32

https://galaxyproject.org/

Copied from original issue: BioContainers/sandbox#20

• ProteoWizard
• SpectraST
• Fido
• Percolator

Looking at the Dockerfile, the biodocker user installs everything locally. I was used to install everything as root. Today I noticed some problem with ADD and premises when I am unpacking/compiling/installing software as non-root in the user local directory.

A container is by itself, if it is dirty for a ./configure; make;make install; who cares ?

We can still use the biodocker user as generic user. Actually for my specific use cases I am mapping the uid e gid to the real users

From @sauloal on September 23, 2015 20:6

Copied from original issue: BioContainers/sandbox#2

From @sauloal on September 24, 2015 14:49

https://github.com/ucdavis-bioinformatics/sickle

Copied from original issue: BioContainers/sandbox#42

From @sauloal on September 24, 2015 19:30

https://github.com/jstjohn/SimSeq

Copied from original issue: BioContainers/sandbox#53

I have the following error:

$ docker run -v //D/processing_data/External/LudovicGillet_SWATH_benchmark/TTOF6600_160305/mzML:/data/ biodckr/dia-umpire java -jar -Xmx8G /home/biodocker/bin/DIA-Umpire/DIA_Umpire_SE.jar /data/lgillet_I160305_001.mzXML /data/diaumpire.se_params

DIA-Umpire singal extraction analysis (version: v1.4256)
2016-03-08 15:16:32,545 INFO [root] Version: v1.4256
2016-03-08 15:16:32,545 INFO [root] Parameter file:/data/diaumpire.se_params
Exception in thread "main" java.io.FileNotFoundException: /data/diaumpire.se_par
ams (No such file or directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.(FileInputStream.java:146)
at java.io.FileInputStream.(FileInputStream.java:101)
at java.io.FileReader.(FileReader.java:58)
at dia_umpire_se.DIA_Umpire_SE.main(DIA_Umpire_SE.java:75)

I guess the error is related with the Windows path.

From @sauloal on September 24, 2015 13:52

Recognising Errors in Assemblies using Paired Reads
https://www.sanger.ac.uk/resources/software/reapr/

Copied from original issue: BioContainers/sandbox#36