Re: [galaxy-dev] building indexes

Have you tried the bwtsw method in the bwa mem data manager? Regarding the 2bit file, even if you make it, are you sure the downstream tool(s) will handle the missing chromosomes/contigs? Maybe you should use the primary assembly instead (at least for the 2bit file). Devon On 10/03/2016

Re: [galaxy-dev] R dependency problems with readline libraries

Is there any part of conda here? This reminds me of the exact same problems that I had with a few libs (readline for example) and conda linkage. On 2016-10-03 13:37, Nicola Soranzo wrote: I suppose this is the same as https://github.com/galaxyproject/tools-devteam/issues/100 , just for a

Re: [galaxy-dev] R dependency problems with readline libraries

I suppose this is the same as https://github.com/galaxyproject/tools-devteam/issues/100 , just for a different R version. Cheers, Nicola On 03/10/16 20:10, Nikolaos Tur wrote: Hi, installation of deseq2 1.10.0 causes next problem:

Re: [galaxy-dev] Install error of package_bioconductor_limma_3_28_10

Hi Nicola, I've created the issue! https://github.com/galaxyproject/tools-iuc/issues/979 Cheers, Alexandre 2016-10-03 12:23 GMT-03:00 Nicola Soranzo : > Hi Alexandre, > thanks for your email! Can you please open an issue for this at >

Re: [galaxy-dev] Install error of package_bioconductor_limma_3_28_10

Hi Alexandre, thanks for your email! Can you please open an issue for this at https://github.com/galaxyproject/tools-iuc/issues/new ? Cheers, Nicola On 03/10/16 15:37, Alexandre Defelicibus wrote: Hi all, I got this error when I tried to install the package

[galaxy-dev] News of the Galaxy: October 2016

Hello all, The *October Galaxy News * is hot off the presses and *upcoming events * are prominent: - *Galaxy training contribution fest

[galaxy-dev] Install error of package_bioconductor_limma_3_28_10

Hi all, I got this error when I tried to install the package package_bioconductor_limma_3_28_10 : Error downloading from URL

[galaxy-dev] building indexes

Hi, I try to build indexes for ch38 (GRCh38.84 Toplevel) using data managers for BWA-MEM and TwoBit. Both failed. Error building index: Error in faToTwoBit, index overflow at CHR_HSCHR4_5_CTG12. The 2bit format does not support indexes larger than 4Gb, please split up into smaller files.