Hello everyone,

I tried to use DESeq2 2015-10-14 (owner iuc) from the toolshed. Unfortunately it does not work. The issue here is that the command line try to find a file that cannot be found :

Fatal error: can't open file '/home/galaxy/Formation/galaxy/dependencies/deseq2/1.8.2/iuc/package_deseq2_1_8_2/00b14423d00f/DESeq2/script/deseq2.R' : No such file or folder

So here the /DESeq2/script/deseq2.R does not exist. I thought about an issue with the path, but the script is nowhere in the galaxy folders. I tried to find the deseq2.R on internet, and created the DESeq2/script/deseq2.R but unfortunately it is not that simple.

Where can I find that deseq2.R ? How can I make this tools work please?

Thank you.

Christ

Hi everyone,

I'll give here what I've done to make it work. I installed libgfortran-4.9-dev, and I had to uninstall then install R. So now I have all the files, I guess. It still doesn't work but the error make me expect something wrong in the input file itself.

Thank you for your help.

Hello,

The problem should go away if the tool is installed with the option to also include required dependencies. You might need to uninstall then reinstall the tool to do this. If you continue to have problems with it, the repository owners can be contacted through the Tool Shed or an issue created at Github.

Best, Jen, Galaxy team

Well, I always ask to galaxy to handle dependencies. Ok i'll try to contact the owners then.

Hi all,

Any news on this? I have the same local install problem on two separate machines. According to the logs the R libs RcppArmadillo, DESeq2 and KernSmooth fail to build/install.

Any solution for this issue?
Thanks
Cristian

I am experiencing a similar problem with DESeq2 in our local Galaxy (Galaxy Tool Version 2.1.8.2).

I installed the tool with a resolve dependency on.
Deseq2 seems to install properly but when I run a test (using the test-data from iuc repo) I get this error

Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Error: package 'RcppArmadillo' could not be loaded

When I  manually source all the package env.sh files and start R I am able to load RcppArmadillo

-------------------------------

source  /ramdisk/galaxy/0.6/tool-dependency/deseq2/1.8.2/iuc/package_deseq2_1_8_2/00b14423d00f/env.sh

source /ramdisk/galaxy/0.6/tool-dependency/R/3.2.1/iuc/package_r_3_2_1/fae49a02a848/env.sh

------------------------

> require("DESeq2")
Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:stats’:

    xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
    do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
    is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unlist, unsplit

Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Rcpp
Loading required package: RcppArmadillo

------------------------------------

I also grep the installation log for error 

-----------------------

grep "error"  /ramdisk/galaxy/0.6/tool-dependency/deseq2/1.8.2/iuc/package_deseq2_1_8_2/00b14423d00f/INSTALLATION.log
g++ -std=c++0x -shared -L/ramdisk/galaxy/0.6/tool-dependency/R/3.2.1/iuc/package_r_3_2_1/fae49a02a848/lib/R/lib -Wl,-rpath,$ORIGIN/../lib -o stringi.so stri_brkiter.o stri_collator.o stri_common.tainer_listraw.o stri_container_listutf8.o stri_ntainer_utf8_indexable.o stri_encoding_conversion.o stri_encoding_detection.o stri_encoding_management.o stri_escape.o stri_exception.o stri_ICU_settings.o stri_join.o stri_length.o stri_pad.o stri_prepare_arg.o stri_random.o stri_reverse.o stri_search_class_count.o stri_search_class_detect.o stri_search_class_extract.o stri_search_class_locate.o stri_search_class_replace.o stri_search_class_split.o stri_search_class_startsendswith.o stri_search_class_subset.o stri_search_class_trim.o stri.o stri_time_symbols.o stri_time_format.o stri_trans_casemap.o stri_trans_other.o stri_trans_normalization.o stri_trans_transliterate.o stri_ucnv.o stri_uloc.o stri_utils.o stri_wrap.o icu55/common/appendable.o icu55/common/bmpset.o icu55/common/brkeng.o icu55/common/brkiter.o icu55/common/bytestream.o icu55/common/bytestriebuilder.o icu55/common/bytestrie.o icu55/common/bytestrieiterator.o icu55/common/caniter.o icu55/common/chariter.o icu55/common/charstr.o icu55/common/dictbe.o icu55/common/dictionarydata.o icu55/common/dtintrv.o icu55/common/errorcode.o icu55/common/filterednormalizer2.o icu55/common/icuplug.o icu55/common/listformatter.o icu55/common/loadednormalizer2impl.o icu55/common/locavailable.o icu55/common/locbased.o icu55/common/locdispnames.o icu55/common/locid.o icu55/common/loclikely.o icu55/common/locresdata.o icu55/common/locutil.o icu55/common/messagepattern.o icu55/common/normalizer2.o icu55/common/normalizer2impl.o icu55/common/normlzr.o icu55/common/parsepos.o icu55/common/patternprops.o icu55/common/propname.o icu55/commcu55/common/umath.o icu55/common/ures_cnv.o icu55/common/uresdata.o icu55/common/usc_impl.o icu55/common/uscript.o icu55/common/ustrfmt.o icu55/common/utf_impl.o icu55/common/utrace.o icu55/common/utypes.o icu55/common/wintz.o icu55/i18n/alphaindex.o icu55/i18n/anytrans.o icu55/i18n/astro.o icu55/i18n/basictz.o icu55/i18n/bocsu.o icu55/i18n/brktrans.o icu55/i18n/buddhcal.o icu55/i18n/calendar.o icu55/i18n/casetrn.o icu55/i18n/cecal.o icu55/i18n/chnsecal.o icu55/i18n/choicfmt.o icu55/i18n/coleitr.o icu55/i18n/collationbuilder.o icu55/i18n/collationcompare.o icu55/i18n/collation.o icu55/i18n/collationdatabuilder.o icu55/i18n/collationdata.o icu55/i18n/collationdatareader.o icu55/i18n/collationdatawriter.o icu55/i18n/collationfastlatinbuilder.o icu55/i18n/collationfastlatin.o icu55/i18n/collationfcd.o icu55/i18n/collationiterator.o icu55/i18n/collationkeys.o icu55/i18n/collationroot.o icu55/i18n/collationrootelements.o icu55/i18n/collationruleparser.o icu55/i18n/collationsets.o icu55/i18n/collationsettings.o icu55/i18n/collationtailoring.o icu55/i18n/collationweights.o icu55/i18n/coll.o icu55/i18n/compactdecimalformat.o icu55/i18n/coptccal.o icu55/i18n/cpdtrans.o icu55/i18n/csdetect.o icu55/i18n/csmatch.o icu55/i18n/csr2022.o icu55/i18n/csrecog.o icu55/i18n/csrmbcs.o icu55/i18n/csrsbcs.o icu55/i18n/csrucode.o icu55/i18n/csrutf8.o icu55/i18n/curramt.o icu55/i18n/currfmt.o icu55/i18n/currpinf.o icu55/i18n/currunit.o icu55/i18n/dangical.o icu55/i18n/datefmt.o icu55/i18n/dcfmtsym.o icu55/i18n/decfmtst.o icu55/i18n/decimalformatpattern.o icu55/i18n/decimfmt.o icu55/i18n/digitlst.o icu55/i18n/dtfmtsym.o icu55/i18n/dtitvfmt.o icu55/i18n/dtitvinf.o icu55/i18n/dtptngen.o icu55/i18n/dtrule.o icu55/i18n/esctrn.o icu55/i18n/ethpccal.o icu55/i18n/filteredbrk.o icu55/i18n/fmtable_cnv.o icu55/i18n/fmtable.o icu55/i18n/format.o icu55/i18n/fphdlimp.o icu55/i18n/fpositer.o icu55/i18n/funcrepl.o icu55/i18n/gender.o icu55/i18n/gregocal.o icu55/i18n/gregoimp.o icu55/i18n/hebrwcal.o icu55/i18n/identifier_info.o icu55/i18n/indiancal.o icu55/i18n/inputext.o icu55/i18n/islamcal.o icu55/i18n/japancal.o icu55/i18n/locdspnm.o icu55/i18n/measfmt.o icu55/i18n/measunit.o icu55/i18n/measure.o icu55/i18n/msgfmt.o icu55/i18n/name2uni.o icu55/i18n/nfrs.o icu55/i18n/nfrule.o icu55/i18n/nfsubs.o icu55/i18n/nortrans.o icu55/i18n/nultrans.o icu55/i18n/numfmt.o icu55/i18n/numsys.o icu55/i18n/olsontz.o icu55/i18n/persncal.o icu55/i18n/plurfmt.o icu55/i18n/plurrule.o icu55/i18n/quant.o icu55/i18n/quantityformatter.o icu55/i18n/rbnf.o icu55/i18n/rbt.o icu55/i18n/rbt_data.o icu55/i18n/rbt

---------------------------

Can someone give me a help to make DESeq2 work?

Thank you very much