Hi Geert and Vipin,

I might also consider the DESeq package and the wrappers from galaxytools if you plan to update your wrappers.

https://github.com/bgruening/galaxytools/tree/master/orphan_tool_dependencies/package_deseq2_1_2_10

@Geert: impressive documentation! Thanks a lot for sharing!
Bjoern


Am 29.07.2014 um 15:54 schrieb Geert Vandeweyer:
I know this is a very old entry to the mailing list, but I thought this
might be useful for some people.

Recently, I set up DESeq-hts and its siblings on our galaxy instance. To
succeed, I performed the steps below.

@vipin: would you consider revising the tool_dependencies.xml for these
tools to take these steps into account? If you're interested, I might
compose a preliminary version.  I believe that most, if not all of these
settings can be automated using the tool_dependencies files.

I did not manage to get DEXSeq working, as it throws errors on the
'estimateDispersions' step in R. I'm not sure how to solve this, as it
gives me the same errors using the demonstration data from the pasilla
library, following the manual steps. (R 3.0.2, bioconductor 2.13, DEXSeq
1.8). Any hints on that are welcome.

Best,

Geert

## GALAXY PACKAGES IN TOOLSHED
#######################
- install the DESeq-hts tools from the main toolshed (cec4b4fb30be from
vipints)
- install R into galaxy (I used package_R_3_0_2 from iuc (50f7e1e71271))
- install package_scipi and package_numpi (from iuc)
- install package_samtools-0.1.18 (I used
devteam/package_samtools_0_1_18/c0f72bdba484)
- install htseq_count package (I used d5edaf8dc974 from lparsons)


## INSTALL DESeq bioconductor package
#########################
- open R from the commandline (using the R version installed earlier !),
install bioconductor package 'DESeq' :
     - source("http://bioconductor.org/biocLite.R";)
     - biocLite('DESeq')
     - biocLite('DESeq2')
     - biocLite('DEXSeq') (needed extra ubuntu package
libcurl4-gnutls-dev for this)


## complie samtools from source (temporary)
#############################
- download samtools 0.1.18 source code into a temporary location and unpack
- compile with : "make CXXFLAGS=-fPIC CFLAGS=-fPIC CPPFLAGS=-fPIC"

## install octave
###########
- OS-dependent, ubuntu: apt-get install octave

## set up DESeq-hts-1.0
###############
- go to
/<path_to_shed_tools>/toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/cec4b4fb30be/deseq_hts/deseq-hts_1.0


- run : "setup_deseq-hts.sh" and provide paths as requested.
     - NOTE: set samtools path to the source compiled version for now
(shed version fails to find sam.h)!!
     - NOTE: also add NumPy path to the SCIPY_PATH variable
     - rest: example (available in bin/deseq_config.sh):
         export LD_LIBRARY_PATH=
         export ENVIRONMENT=galaxy
         export DESEQ_VERSION=1.12.1
         export
DESEQ_PATH=/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/cec4b4fb30be/deseq_hts/deseq-hts_1.0

         export
DESEQ_SRC_PATH=/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/cec4b4fb30be/deseq_hts/deseq-hts_1.0/src

         export
DESEQ_BIN_PATH=/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/cec4b4fb30be/deseq_hts/deseq-hts_1.0/bin

         export INTERPRETER=octave
         export MATLAB_BIN_PATH=
         export MATLAB_MEX_PATH=
         export MATLAB_INCLUDE_DIR=
         export OCTAVE_BIN_PATH=/opt/software/octave-3.8.0/bin/octave
         export OCTAVE_MKOCT=/opt/software/octave-3.8.0/bin/mkoctfile
         export SAMTOOLS_DIR=/galaxy/packages_sources/samtools-0.1.18_fPIC
         #export
SAMTOOLS_DIR=/galaxy/galaxy_tool_binaries/samtools/0.1.18/devteam/package_samtools_0_1_18/c0f72bdba484/bin/

         export PYTHON_PATH=/galaxy/galaxy_env/bin/python
         export
SCIPY_PATH=/galaxy/galaxy_tool_binaries/scipy/0.12.0/iuc/package_scipy_0_12/984d208b0808/lib/python/:/galaxy/galaxy_tool_binaries/numpy/1.7.1/iuc/package_numpy_1_7/ef12a3a11d5b/lib/python/

     ## USE THE TOOLSHED VERSION, The one you installed bioclite
packages with.
         export
R_PATH=/galaxy/galaxy_tool_binaries/R_3_0_2/3.0.2/iuc/package_r_3_0_2/50f7e1e71271/R


- enter mex directory, run "make octave"
- swap SAMTOOLS_DIR in bin/deseq_config.sh to point to the toolshed
version of samtools 0.1.18

## RUN DESeq-hts-1.0 TEST
##################
enter src directory, run test from the toolconf xml file:
"./deseq-hts.sh ../test_data/deseq_c_elegans_WS200-I-regions.gff3
../test_data/deseq_c_elegans_WS200-I-regions_deseq.txt
../test_data/genes.mat
../test_data/deseq_c_elegans_WS200-I-regions-SRX001872.bam
../test_data/deseq_c_elegans_WS200-I-regions-SRX001875.bam"


## set up DESeq-hts-2.0
###############
- go to
/<path_to_shed_tools>/toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/cec4b4fb30be/deseq_hts/deseq-hts_2.0

- similar to 1.0: setup config file,
     - point to src compiled version of samtools
     - add scipy and numpy to scipi_path variable
     - use the toolshed version of R
- in mex, run "make octave"
- swap samtools path

IMPORTANT:
----------------
- open "src/deseq2-hts.sh" in a text editor and add an extra line after
line 38 (echo load the genome annotation....):
         export PYTHONPATH=$PYTHONPATH:${SCIPY_PATH}
- in the same file (src/deseq2-hts.sh), append line 70
(../bin/get_read_counts...) with 2>&1  . This prevents some octave
warnings from crashing the job (missing docstring warnings)


Test-run in galaxy seems to work.

## set up DEXSeq-hts-1.0
###############
go to
/<path_to_shed_tools>/toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/cec4b4fb30be/deseq_hts/dexseq_1.0

run setup_dexseq-hts.sh
   - set samtools path
   - set python_path : I use the galaxy python version
(/galaxy/galaxy_env/bin/python), see development docs
   - set pythonpath: Make sure to include both HTSeq AND numpy here ! :
         export
PYTHONPATH=/galaxy/galaxy_tool_binaries/htseq/0.5.4p5/lparsons/htseq_count/3ffe4e2572a7/lib/python/HTSeq-0.5.4p5-py2.6-linux-x86_64.egg:/galaxy/galaxy_tool_binaries/numpy/1.7.1/iuc/package_numpy_1_7/ef12a3a11d5b/lib/python:$PYTHONPATH

   - set R_path : I use toolshed version package_r_3_0_2 from iuc (with
the installed bioclite packages from above)

=> FAILS : crashes on estimateDispersions / fitDispersionFunction step
in run_DEXseq.R


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