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Old 07-05-2011, 06:36 AM   #1
markero
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Default python and NGS data

Hi all,
I am wondering how many python packages are available for NGS data analysis.
As far as I know, HTSeq and Erange are written in python.
Any others?
Thanks a lot!
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Old 07-06-2011, 02:28 AM   #2
maubp
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Biopython has support for SFF, FASTQ, FASTA + QUAL - handy for simple manipulation of input data. Also has an ACE parser if you are getting those from your assemblies.
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Old 06-29-2013, 12:48 PM   #3
Gus
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You may want to check out my blacktie pipeline. It combines all data and commands to automate running the tuxedo protocol: tophat/cufflinks/cummerbund.

http://blacktie.readthedocs.org/en/latest/
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Old 07-02-2013, 07:52 AM   #6
Gus
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Quote:
Originally Posted by crazyhottommy View Post
some of my collections:
btw; blacktie is also one of my collections
Thats great! If you find anything that needs attention or even just want to request a new feature, PLEASE file an issue at https://github.com/xguse/blacktie/issues!

I am eager to improve blacktie but I need user input!

Thanks,

Gus
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Old 05-15-2014, 07:13 AM   #7
csmatyi
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Hi, maybe you can help me with an installation problem I have with bcbio-nextgen. I want to install it on linux, but I get this error:

-----

Error: Cannot install tabix because conflicting formulae are installed.

htslib: because tabix and bgzip binaries are now part of the HTSlib project

Please `brew unlink htslib` before continuing.

Unlinking removes a formula's symlinks from /home/unmc_cbsb/matt/bin/bcbio. You can
link the formula again after the install finishes. You can --force this
install, but the build may fail or cause obscure side-effects in the
resulting software.

Fatal error: local() encountered an error (return code 1) while executing 'export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/home/unmc_cbsb/matt/bin/bcbio/lib/perl5:${PERL5LIB} && /home/unmc_cbsb/matt/bin/bcbio/bin/brew install --env=inherit tabix'

Aborting.
Traceback (most recent call last):
File "bcbio_nextgen_install.py", line 253, in <module>
main(parser.parse_args(), sys.argv[1:])
File "bcbio_nextgen_install.py", line 41, in main
subprocess.check_call([bcbio["bcbio_nextgen.py"], "upgrade"] + _clean_args(sys_argv, args, bcbio))
File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/lustre/work/unmc_cbsb/matt/bcbio-nextgen/anaconda/bin/bcbio_nextgen.py', 'upgrade', '--tooldir=/home/unmc_cbsb/matt/bin/bcbio', '--nosudo', '--isolate', '--data']' returned non-zero exit status 1

-----

the command I use at installation is:

python bcbio_nextgen_install.py /lustre/work/unmc_cbsb/matt/bcbio-nextgen --tooldir=/home/unmc_cbsb/matt/bin/bcbio --nosudo --isolate

Thanks in advance for any help.
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Old 05-15-2014, 01:12 PM   #8
crazyhottommy
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Quote:
Originally Posted by csmatyi View Post
Hi, maybe you can help me with an installation problem I have with bcbio-nextgen. I want to install it on linux, but I get this error:

-----

Error: Cannot install tabix because conflicting formulae are installed.

htslib: because tabix and bgzip binaries are now part of the HTSlib project

Please `brew unlink htslib` before continuing.

Unlinking removes a formula's symlinks from /home/unmc_cbsb/matt/bin/bcbio. You can
link the formula again after the install finishes. You can --force this
install, but the build may fail or cause obscure side-effects in the
resulting software.

Fatal error: local() encountered an error (return code 1) while executing 'export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/home/unmc_cbsb/matt/bin/bcbio/lib/perl5:${PERL5LIB} && /home/unmc_cbsb/matt/bin/bcbio/bin/brew install --env=inherit tabix'

Aborting.
Traceback (most recent call last):
File "bcbio_nextgen_install.py", line 253, in <module>
main(parser.parse_args(), sys.argv[1:])
File "bcbio_nextgen_install.py", line 41, in main
subprocess.check_call([bcbio["bcbio_nextgen.py"], "upgrade"] + _clean_args(sys_argv, args, bcbio))
File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/lustre/work/unmc_cbsb/matt/bcbio-nextgen/anaconda/bin/bcbio_nextgen.py', 'upgrade', '--tooldir=/home/unmc_cbsb/matt/bin/bcbio', '--nosudo', '--isolate', '--data']' returned non-zero exit status 1

-----

the command I use at installation is:

python bcbio_nextgen_install.py /lustre/work/unmc_cbsb/matt/bcbio-nextgen --tooldir=/home/unmc_cbsb/matt/bin/bcbio --nosudo --isolate

Thanks in advance for any help.
see a post here
http://bcbio.wordpress.com/2014/03/0...s-with-docker/
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Old 05-16-2014, 11:27 AM   #9
csmatyi
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Hi crazyhottommy,

I have no sudo privilege on the server I'm on.
Basically, how do I install it in a simple way without any special necessary privileges needed?
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