Hey Greet and Bjoern,

Sorry for the troubles with dependencies during the automated installation
procedure!
I will add tool dependency file, when I get some time during this weekend
:)

Vipin | Rätsch Lab


On Tue, Jul 29, 2014 at 10:06 AM, Björn Grüning <bjoern.gruen...@gmail.com>
wrote:

> 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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