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MerrimanLab / selectionTools

Pipeline to take VCF through to Selection Analysis.
MIT License
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Problem with install.sh / python #12

Open semassey opened 9 years ago

semassey commented 9 years ago

hi - thanks for writing this pipeline and I am looking forward to using it. I ran the install.sh script and produced the following error message:

python: can't open file 'setup.py': [Errno 2] No such file or directory error with python

This is on CentOS 6 with python 2.6.6. I tried running python 2.7 on the setup.py script

eg. /usr/local/Python2.7/python setup.py

and received the following message :+1: Traceback (most recent call last): File "setup.py", line 1, in from setuptools import setup, find_packages ImportError: No module named setuptools

however, setuptools is present (python-setuptools-0.6.10-3.el6.noarch)

any help much appreciated

Steve

murraycadzow commented 9 years ago

Hi Steve,

It could be that setup tools is either too old or not configured with your 2.7 installation perhaps you could try and install an updated version using this tutorial (https://www.digitalocean.com/community/tutorials/how-to-set-up-python-2-7-6-and-3-3-3-on-centos-6-4)

If you can't get the pipeline installed through the normal means, I have recently made a docker container that you could try (docker directory of the repo)

Murray

semassey commented 9 years ago

Thanks Murray

that fixed it

btw. the PyVCF and pyfasta directories were empty in the main package - so I downloaded these separately from the github page

cheers,

steve

On 23 April 2015 at 19:01, murraycadzow notifications@github.com wrote:

Hi Steve,

It could be that setup tools is either too old or not configured with your 2.7 installation perhaps you could try and install an updated version using this tutorial ( https://www.digitalocean.com/community/tutorials/how-to-set-up-python-2-7-6-and-3-3-3-on-centos-6-4 )

If you can't get the pipeline installed through the normal means, I have recently made a docker container that you could try (docker directory of the repo)

Murray

— Reply to this email directly or view it on GitHub https://github.com/smilefreak/selectionTools/issues/12#issuecomment-95740927 .

Steven E Massey Associate Professor of Bioinformatics Biology Department, PO Box 23360 University of Puerto Rico - Rio Piedras San Juan PR 00931

Tel: 7875984859 (Cell), 7877640000 x7798 (Lab), x2556 (Office) Bioinformatics Lab NCN 343B, Office FB 246 E-mail: stevenemassey@gmail.com Web-page: www.scanmoment.org/masseybioinformatics-UPR.html

semassey commented 9 years ago

hi Murray

I've been running selectiontools, but had the following problem. When the pipeline begins to run qctool it gives the following error message and terminates:

/opt/selectiontools/selectionTools-master/bin/qctool: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /opt/selectiontools/selectionTools-master/bin/qctool)

I built glibc2.14 and linked to it using LD_LIBRARY_PATH and LIBRARY_PATH. Shapeit also requires this library and runs fine within the pipeline. Also, qctool runs fine when run outside the pipeline. I also set LD_LIBRARY_PATH in the run_pipeline.py script, but I still received the same error message and the pipeline terminated. Do you have any ideas how to fix this ? I think there must be a simple solution...

thanks

steve

On 24 April 2015 at 15:01, Steven E Massey stevenemassey@gmail.com wrote:

Thanks Murray

that fixed it

btw. the PyVCF and pyfasta directories were empty in the main package - so I downloaded these separately from the github page

cheers,

steve

On 23 April 2015 at 19:01, murraycadzow notifications@github.com wrote:

Hi Steve,

It could be that setup tools is either too old or not configured with your 2.7 installation perhaps you could try and install an updated version using this tutorial ( https://www.digitalocean.com/community/tutorials/how-to-set-up-python-2-7-6-and-3-3-3-on-centos-6-4 )

If you can't get the pipeline installed through the normal means, I have recently made a docker container that you could try (docker directory of the repo)

Murray

— Reply to this email directly or view it on GitHub https://github.com/smilefreak/selectionTools/issues/12#issuecomment-95740927 .

Steven E Massey Associate Professor of Bioinformatics Biology Department, PO Box 23360 University of Puerto Rico - Rio Piedras San Juan PR 00931

Tel: 7875984859 (Cell), 7877640000 x7798 (Lab), x2556 (Office) Bioinformatics Lab NCN 343B, Office FB 246 E-mail: stevenemassey@gmail.com Web-page: www.scanmoment.org/masseybioinformatics-UPR.html

Steven E Massey Associate Professor of Bioinformatics Biology Department, PO Box 23360 University of Puerto Rico - Rio Piedras San Juan PR 00931

Tel: 7875984859 (Cell), 7877640000 x7798 (Lab), x2556 (Office) Bioinformatics Lab NCN 343B, Office FB 246 E-mail: stevenemassey@gmail.com Web-page: www.scanmoment.org/masseybioinformatics-UPR.html

murraycadzow commented 9 years ago

Hi Steve,

Have you replaced the qctool that came with the pipeline with the one you built? I know that we have had that problem when using REHL, the version that is automatically used doesn't work and gives that error but downloading the REHL version of qctool and completely replacing it works. Also just check the path that is given in the config file you are using is going to the working version

Murray

semassey commented 9 years ago

thanks, I used the the scientific-linux binary, v1.4, and it works fine now

steve

On 3 May 2015 at 18:56, murraycadzow notifications@github.com wrote:

Hi Steve,

Have you replaced the qctool that came with the pipeline with the one you built? I know that we have had that problem when using REHL, the version that is automatically used doesn't work and gives that error but downloading the REHL version of qctool and completely replacing it works. Also just check the path that is given in the config file you are using is going to the working version

Murray

— Reply to this email directly or view it on GitHub https://github.com/smilefreak/selectionTools/issues/12#issuecomment-98553823 .

Steven E Massey Associate Professor of Bioinformatics Biology Department, PO Box 23360 University of Puerto Rico - Rio Piedras San Juan PR 00931

Tel: 7875984859 (Cell), 7877640000 x7798 (Lab), x2556 (Office) Bioinformatics Lab NCN 343B, Office FB 246 E-mail: stevenemassey@gmail.com Web-page: www.scanmoment.org/masseybioinformatics-UPR.html

semassey commented 9 years ago

Dear Murray

I've run the pipeline on an autosome and would now like to run it on the X chromosome. I was wondering what changes I would have to make to do that. Firstly, I'll need to use the --chrX option of Shapeit, and I'm guessing I need to alter the run scripts. Secondly, I would need to use a genetic map. I have three available, but was not sure which one to use. They are:

genetic_map_chrX_PAR1_combined_b37.txt genetic_map_chrX_PAR2_combined_b37.txt genetic_map_chrX_nonPAR_combined_b37.txt

many thanks for your help

steve

On 4 May 2015 at 18:14, Steven E Massey stevenemassey@gmail.com wrote:

thanks, I used the the scientific-linux binary, v1.4, and it works fine now

steve

On 3 May 2015 at 18:56, murraycadzow notifications@github.com wrote:

Hi Steve,

Have you replaced the qctool that came with the pipeline with the one you built? I know that we have had that problem when using REHL, the version that is automatically used doesn't work and gives that error but downloading the REHL version of qctool and completely replacing it works. Also just check the path that is given in the config file you are using is going to the working version

Murray

— Reply to this email directly or view it on GitHub https://github.com/smilefreak/selectionTools/issues/12#issuecomment-98553823 .

Steven E Massey Associate Professor of Bioinformatics Biology Department, PO Box 23360 University of Puerto Rico - Rio Piedras San Juan PR 00931

Tel: 7875984859 (Cell), 7877640000 x7798 (Lab), x2556 (Office) Bioinformatics Lab NCN 343B, Office FB 246 E-mail: stevenemassey@gmail.com Web-page: www.scanmoment.org/masseybioinformatics-UPR.html

Steven E Massey Associate Professor of Bioinformatics Biology Department, PO Box 23360 University of Puerto Rico - Rio Piedras San Juan PR 00931

Tel: 7875984859 (Cell), 7877640000 x7798 (Lab), x2556 (Office) Bioinformatics Lab NCN 343B, Office FB 246 E-mail: stevenemassey@gmail.com Web-page: www.scanmoment.org/masseybioinformatics-UPR.html

murraycadzow commented 9 years ago

Hi Steve,

I haven't actually done any work with the sex chromosomes and I think it may require a little tweaking to get the pipeline to work. I would phase using shapeit outside of the pipeline and then use those haps and sample files for the pipeline (if you need to impute there may be an extra tweak needed). The pipeline uses a numeric value for chromosomes similar to plink so I would use -c 23, also in your reference files I think to prevent potential issues I would make a duplicate copy of the X reference files and change all references to X to be 23

As for what maps to use take a look at these, it looks like you would end up using all 3 but I don't know how you would go about it within the pipeline context http://mathgen.stats.ox.ac.uk/impute/chromosome_X_options.html http://mathgen.stats.ox.ac.uk/impute/README_1000G_phase1interim_jun2011.txt

Murray

semassey commented 9 years ago

Thanks a lot Murray, I'll let you know how it goes

On 7 May 2015 at 22:33, murraycadzow notifications@github.com wrote:

Hi Steve,

I haven't actually done any work with the sex chromosomes and I think it may require a little tweaking to get the pipeline to work. I would phase using shapeit outside of the pipeline and then use those haps and sample files for the pipeline (if you need to impute there may be an extra tweak needed). The pipeline uses a numeric value for chromosomes similar to plink so I would use -c 23, also in your reference files I think to prevent potential issues I would make a duplicate copy of the X reference files and change all references to X to be 23

As for what maps to use take a look at these, it looks like you would end up using all 3 but I don't know how you would go about it within the pipeline context http://mathgen.stats.ox.ac.uk/impute/chromosome_X_options.html http://mathgen.stats.ox.ac.uk/impute/README_1000G_phase1interim_jun2011.txt

Murray

— Reply to this email directly or view it on GitHub https://github.com/smilefreak/selectionTools/issues/12#issuecomment-100077590 .

Steven E Massey Associate Professor of Bioinformatics Biology Department, PO Box 23360 University of Puerto Rico - Rio Piedras San Juan PR 00931

Tel: 7875984859 (Cell), 7877640000 x7798 (Lab), x2556 (Office) Bioinformatics Lab NCN 343B, Office FB 246 E-mail: stevenemassey@gmail.com Web-page: www.scanmoment.org/masseybioinformatics-UPR.html