[galaxy-dev] Bowtie2 index building

Hello, I am trying to build Bowtie2 index for hg19. I a using Docker image of Galaxy. Computer I am using have 12 cores and 64 GB of RAM. Error I am getting is: Fatal error: Exit code 1 () Building a SMALL index Could not allocate space for a joined string of 2897310462 elements. Switching to a

Re: [galaxy-dev] Bowtie2 index building

...@gmail.com>> wrote: Hi Deepak, how are you running this Container? Can you check how many memory you have inside the container? Cheers, Bjoern On 11.08.2017 15:35, Deepak Tanwar wrote: Hello, I am trying to build Bowtie2 index for hg19. I a using Docker image of Galaxy. Computer I am using h

Re: [galaxy-dev] Bowtie2 index building

Also, I am running this container on a Mac Pro using Kitematic and I have docker preference set to use 12 cores and 64 GB RAM. Thanks, Deepak On Aug 11, 2017, at 9:54 AM, Deepak Tanwar mailto:dktan...@hotmail.com>> wrote: Hi Björn, If I do docker stats: CONTAINER

Re: [galaxy-dev] Bowtie2 index building

e configs. > Sorry to be not more helpful! > Bjoern > > On 11.08.2017 15:55, Deepak Tanwar wrote: >> Also, I am running this container on a Mac Pro using Kitematic and I >> have docker preference set to use 12 cores and 64 GB RAM. >> >> Thanks, >>

[galaxy-dev] Samtools problem in Docker

Hello everyone, I am facing problem in uploading bam files on Galaxy. I am using Docker image of Galaxy. I have installed samtools version 0.1.19 and added it to the path /tool_deps/samtools/0.1.19/iuc/package_samtools_0_1_19/c9bd782f5342/bin/samtools Error: Exception: Attempting to use functi

Re: [galaxy-dev] Samtools problem in Docker

:08 PM, Deepak Tanwar mailto:dktan...@hotmail.com>> wrote: Hello everyone, I am facing problem in uploading bam files on Galaxy. I am using Docker image of Galaxy. I have installed samtools version 0.1.19 and added it to the path /tool_deps/samtools/0.1.19/iuc/package_samtools_0_1_19/c9bd

Re: [galaxy-dev] Samtools problem in Docker

oaded successfully! On Aug 14, 2017, at 16:58, Björn Grüning mailto:bjoern.gruen...@gmail.com>> wrote: Hi Deepak, as Peter mentioned the Galaxy Docker container can be used as it is. Can you provide the original error message from the TS? Cheers, Bjoern On 14.08.2017 18:17, Deepak

[galaxy-dev] plane error for Rscript

Hello everyone, I have a question about https://github.com/nturaga/bioc-galaxy-integration I am trying to convert a RScript into a Galaxy tool. planemo bioc_tool_init --rscript ./countsAroundTSS.R --input ENCFF027UTM.bam --input mm10 --input 500 --input 500 --input transcripts_mm10_UCSC.sqlite

[galaxy-dev] MACS2 Error

Hi all, There is some problem with MACS2: export/galaxy-central/database/job_working_directory/000/380/tool_script.sh: line 25: macs2: command not found Fatal error: Exit code 127 () Tool installed: /shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2

Re: [galaxy-dev] MACS2 Error

Hello, I am still facing problem. I have tried to reinstall MACS2 but nothing helped. Thank you! Deepak On Oct 16, 2017, at 4:00 PM, Deepak Tanwar mailto:dktan...@hotmail.com>> wrote: Hi all, There is some problem with MACS2: export/galaxy-central/database/job_working_directory/0

Re: [galaxy-dev] MACS2 Error

Also check the conda activation log file (under working/ I think) in that directory to see if it has anything useful. Devon On 10/18/2017 05:46 PM, Deepak Tanwar wrote: Hello, I am still facing problem. I have tried to reinstall MACS2 but nothing helped. Thank you! Deepak On Oct 16, 2017,

[galaxy-dev] Job error

Hi all, I am facing some problem in building a galaxy tool from Rscript (using planemo). The error file is attached. Main error is: dyld: Library not loaded: @rpath/libintl.8.dylib I have tried suggestions from: https://github.com/tectonic-typesetting/tectonic/issues/40 Thank you, Deepak

Re: [galaxy-dev] Job error

Sorry, forgot to attach the error file! On Oct 20, 2017, at 12:21 PM, Deepak Tanwar mailto:dktan...@hotmail.com>> wrote: Hi all, I am facing some problem in building a galaxy tool from Rscript (using planemo). The error file is attached. Main error is: dyld: Library not loaded:

[galaxy-dev] Bioconductor packages in Galaxy

Hi, I am using galaxy via Docker. I cannot find saw package on galaxy toolshed. It is available on bioconda: https://bioconda.github.io/recipes/bioconductor-csaw/README.html How can I use it Galaxy? Thank you, Deepak On Nov 22, 2017, at 05:03, Gildas Le Corguillé mailto:lecorgui...@sb-roscof