rna-seq document

[kspham]

Excited to try the new bcbio-nexgen just updated yesterday on RNA-seq data. There is a minor issue: In the description of the default RNA-seq pipeline, alientrimmer should be used but I see the current pipeline is running cutadapt. Thank you!

[roryk]

Hi Son,

Thanks for the report. It will default to cutadapt if AlienTrimmer isn't installed-- you can get AlienTrimmer by running a bcbio_nextgen.py upgrade --tools. Let me know if that doesn't swap over for you.

Thanks!

[kspham]

This is the last output from bcbio_nextgen.py upgrade --tools I don't know if it's a successful run or it failed.

[localhost] local: /home/snow/bin/bcbio/tool/bin/brew info rna-star DBG [config.py]: Using config file /home/snow/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/r-libs.yaml [localhost] local: touch install_packages.R [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "mkdir -p /home/snow/bin/bcbio/tool/lib/R/site-library" [localhost] local: echo ' .libPaths(c("/home/snow/bin/bcbio/tool/lib/R/site-library")) cran.repos <- getOption("repos") cran.repos["CRAN" ] <- "http://cran.fhcrc.org/" options(repos=cran.repos) source("http://bioconductor.org/biocLite.R") ' >> "$(echo install_packages.R)" [localhost] local: echo ' repo.installer <- function(repos, install.fn) {

update.packages(lib.loc="/home/snow/bin/bcbio/tool/lib/R/site-library", repos=repos, ask=FALSE)

  maybe.install <- function(pname) {
    if (!(pname %in% installed.packages()))
      install.fn(pname)
  }
}
' >> "$(echo install_packages.R)"

[localhost] local: echo ' std.pkgs <- c("ggplot2", "gsalib", "snow") std.installer = repo.installer(cran.repos, install.packages) lapply(std.pkgs, std.installer) ' >> "$(echo install_packages.R)" [localhost] local: echo ' bioc.pkgs <- c("cn.mops", "rtracklayer") bioc.installer = repo.installer(biocinstallRepos(), biocLite) lapply(bioc.pkgs, bioc.installer) ' >> "$(echo install_packages.R)" [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "Rscript install_packages.R" Bioconductor version 2.13 (BiocInstaller 1.12.1), ?biocLite for help A newer version of Bioconductor is available after installing a new version of R, ?BiocUpgrade for help [[1]] NULL

[[2]] NULL

[[3]] NULL

[[1]] NULL

[[2]] NULL

[localhost] local: rm -f install_packages.R Creating manifest of installed packages in /usr/local/share/bcbio-nextgen/manifest

On Wed, Apr 23, 2014 at 10:39 AM, Rory Kirchner notifications@github.comwrote:

Hi Son,

Thanks for the report. It will default to cutadapt if AlienTrimmer isn't installed-- you can get AlienTrimmer by running a bcbio_nextgen.py upgrade --tools. Let me know if that doesn't swap over for you.

Thanks!

— Reply to this email directly or view it on GitHubhttps://github.com/chapmanb/bcbio-nextgen/issues/411#issuecomment-41191474 .

[roryk]

Hi Son,

I added some more useful messages to the end of the upgrade so it is clear that it finished. Thanks for the reports, it is really helpful and we really appreciate it.

[kspham]

Roryk: It still uses cutadapt after the upgrade.

[roryk]

Hi Son,

Is AlienTrimmer in the share/java directory, where bcbio-nextgen installs GATK and the like?

[kspham]

Hi Roryk: This is the content of the folder: AlienTrimmer AlienTrimmer-0.3.2 bcbio_variation bcbio_variation-0.1.3 bcbio_variation-0.1.5 cramtools-2.1.jar gatk gatk-2.3-9-gdcdccbb gatk-2.8-1-g932cd3a gatk-framework.jar gatk-nightly-2014-02-03-gc6765ad mutect mutect-1.1.5 picard picard-1.96 RNA-SeQC RNA-SeQC-1.1.7 RTG.jar snpeff snpeff-3_4 varscan varscan-2.3.6 ~

[kspham]

Rory: I tried to remove the try catch code and use only AlienStrimmer , here is the message: File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/bam/trim.py", line 33, in trim_adapters jarpath = config_utils.get_program("AlienTrimmer", config, "dir") File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/config_utils.py", line 177, in get_program return _get_program_dir(name, pconfig) File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/config_utils.py", line 220, in _get_program_dir raise ValueError("Could not find directory in config for %s" % name) ValueError: Could not find directory in config for AlienTrimmer

[roryk]

Hi Son,

Thanks for the awesome detective work. Drat-- is AlienTrimmer not added to your bcbio_system.yaml file? Here is the lines that need to get added: https://github.com/chapmanb/bcbio-nextgen/blob/master/config/bcbio_system.yaml#L67.

I'm not sure what triggers an update of that file on upgrade, @chapmanb will know.

[kspham]

Works great, at least, it's using AlienTrimmer now :)

[roryk]

Great, thanks Son.

[chapmanb]

Son; Sorry about the problems. For now you'll have to manually add in new tools to existing bcbio_system files. I generally try to avoid re-writing them too much to avoid accidentally introducing something new.

One of the things on my todo list is to more gracefully handle this by being able to look for the files in "well-known" standard places that the installers put them. Glad things are working now and sorry again about the confusion.