Question: DESeq2 file missing
gravatar for christophe.habib
3.1 years ago by
christophe.habib340 wrote:

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.




file missing deseq2 • 1.6k views
ADD COMMENTlink modified 2.8 years ago by david.a.morais110 • written 3.1 years ago by christophe.habib340
gravatar for christophe.habib
3.1 years ago by
christophe.habib340 wrote:

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.

ADD COMMENTlink written 3.1 years ago by christophe.habib340
gravatar for Jennifer Hillman Jackson
3.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:


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

ADD COMMENTlink written 3.1 years ago by Jennifer Hillman Jackson25k

How can I contact owners through the Tool Shed please?

ADD REPLYlink written 3.1 years ago by christophe.habib340

Please see comment on the post below.

ADD REPLYlink written 3.1 years ago by Jennifer Hillman Jackson25k

It's more or less me. Can you please check the file INSTALLTION.log inside of your deseq2 installation. It seems that DESEq2 is not installed properly. Unfortunately, R did not fail properly if it fails. We fixed this in the development version of Galaxy. Now it fails as it should be ... but we need to find the root cause of why this is failing for you.

ADD REPLYlink written 3.1 years ago by Bjoern Gruening5.1k

Hi Bjoern,

The file is HUGE and I don't really know what I am supposed to search.

In the INSTALLATION.log file in "/Formation/galaxy/dependencies/deseq2/1.8.2/iuc/package_deseq2_1_8_2/00b14423d00f$" I have this when I grep "error"

And when I grep "warning" I have this : 

But I don't really get what I can do to make things work.. I hope you will understand this more than me.

Thank you for your help!

ADD REPLYlink written 3.1 years ago by christophe.habib340

Can you send me this file via mail?

ADD REPLYlink written 3.1 years ago by Bjoern Gruening5.1k

Sure, I sent this to your gmail, if I didn't make mistake on your adress.

ADD REPLYlink written 3.1 years ago by christophe.habib340
gravatar for christophe.habib
3.1 years ago by
christophe.habib340 wrote:

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

ADD COMMENTlink written 3.1 years ago by christophe.habib340

There could be an install problem and the IUC can help to determine the root cause. To contact through the Tool Shed, first log in, then use the upper right menu "Repository Actions". One choice is to send a message to the repo owners.

Include where you are installing (local or cloud), the Galaxy version, and anything else you have done to customize your instance. This will get things started and they'll ask for more specifics if needed.

Hope this works out! Jen

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by Jennifer Hillman Jackson25k
gravatar for tuto345
3.0 years ago by
tuto34520 wrote:

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?

ADD COMMENTlink written 3.0 years ago by tuto34520

Sorry, should have included more info: 

Latest stable galaxy release newly installed on Centos 7.

In the INSTALLATION.log, for the 3 libs, I have

* checking LAPACK_LIBS: divide-and-conquer complex SVD available via system LAPACK
g++ -I/home/galaxy/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/fae49a02a848/lib/R/include -DNDEBUG  -I/usr/local/include -I"/home/galaxy/galaxy/dependency_dir/deseq2/1.8.2/iuc/package_deseq2_1_8_2/00b14423d00f/Rcpp/include"  -I../inst/include -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
2_1_8_2/00b14423d00f/Rcpp/include"  -I../inst/include -fpic  -g -O2  -c fastLm.cpp -o fastLm.o
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  /home/galaxy/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/fae49a02a848/lib/R/lib/../lib/ version `GFOExecution halted

ERROR: dependency ‘RcppArmadillo’ is not available for package ‘DESeq2’

gcc -std=gnu99 -shared -L/home/galaxy/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/fae49a02a848/lib/R/lib -Wl,-rpath,$ORIGIN/../lib -o blkest.o cp.o dgedi.o dgefa.o dgesl.o init.o linbin.o linbin2D.o locpoly.o rlbin.o sdiag.o sstdiag.o -lblas -lgfortran -lm -lgfortran -lm -L/home/galaxy/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/fae49a02a848/lib/R/lib -lR
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/home/galaxy/galaxy/dependency_dir/deseq2/1.8.2/iuc/package_deseq2_1_8_2/00b14423d00f/KernSmooth/libs/':
  /home/galaxy/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/fae49a02a848/lib/R/lib/../lib/ version `GFORTRAN_1.4' not found (required by /lib64/
Execution halted



ADD REPLYlink written 3.0 years ago by tuto34520
gravatar for david.a.morais
2.8 years ago by
david.a.morais110 wrote:

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

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 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/

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


> 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’:


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

    anyDuplicated, append,, as.vector, cbind, colnames,, duplicated, eval, evalq, Filter, Find, get, intersect,
    is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,, pmin,, Position, rank, rbind, Reduce,,
    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 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


ADD COMMENTlink written 2.8 years ago by david.a.morais110

Can you share your INSTALLATION.log file with us?

ADD REPLYlink written 2.8 years ago by Bjoern Gruening5.1k

Hi Bjoern
Do you want me to paste the whole file here or you have an email I can send it to?


ADD REPLYlink written 2.8 years ago by david.a.morais110

I sent it to your gmail.


ADD REPLYlink written 2.8 years ago by david.a.morais110

Hi Bjoern,

Have you receive my INSTALLATION.log?


ADD REPLYlink written 2.8 years ago by david.a.morais110

Sorry for my late response, please check your inbox :)

ADD REPLYlink written 2.7 years ago by Bjoern Gruening5.1k

Hi Bjoern,

Thanks again for your help. It led me to find out the problem.

It seems that Deseq was not sourcing


Instead it was using /usr/bin/R. That's why when I tried manually sourcing all files it worked and via Galaxy interface it did not.

I just added this line

if [ -f /ramdisk/galaxy/0.6/tool-dependency/R/3.2.1/iuc/package_r_3_2_1/fae49a02a848/ ] ; then . /ramdisk/galaxy/0.6/tool-dependency/R/3.2.1/iuc/package_r_3_2_1/fae49a02a848/ ; fi



And now the tool is working as intended.

Thank you so much for your help. I really appreciated


ADD REPLYlink written 2.7 years ago by david.a.morais110
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