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Blacktie: a streamlined interface to the popular tophat/cufflinks RNA-seq pipeline

Home Page: https://blacktie.readthedocs.org/en/latest/

License: GNU General Public License v3.0

Python 52.56% CSS 10.26% JavaScript 34.00% Shell 3.18%

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tastysquirrel jrherr snewhouse kmurphy12 srividya22

blacktie's Issues

add bowtie/bowtie2 automation to the pipeline

make no emailing the default (change --no-email to --send-updates)

--prog should take multiple steps rather than just ONE or 'all'

Currently updating argparse call to allow any number of allowed programs to call.

However, you are still in charge of making sure that the required files exist where they should be for steps that have not JUST had the correct preceding command called.

Tell user where qsub scripts were written

when using --mode=qsub_script print location of scripts to user's screen

automate running of qsubs with dependencies on SGE

as of now:

blacktie --prog all config.yaml --mode qsub_script

writes your individual qsub scripts but you have to submit them all by hand.

blacktie should be able to write a meta-qsub that will take care of submitting, monitoring successfull completion of dependent runs and progression to the next set of qsubs.

cummerbund not included in dry run when "--prog all"

Hi,

Looks like a great program! I've run into a small problem when calling cummerbund.

When I run the following cummerbund is not listed as an output.
blacktie --prog all --no-email --mode dry_run path/example.yaml

However the following works just fine:
blacktie --prog cummerbund --no-email --mode dry_run path/example.yaml

I haven't run anything through, only in dry_run. Is there a reason that cummerbund is not listed in the dry_run, or is the "all" call not working correctly?

Thank you. All the best,
Bobby

blacktie --prog all ../../config_files/tophat_cufflinks_Cq_0-4-6-8-10.gtf_strict.hpc.yaml --mode qsub_script
[Note] Starting tophat step.

[Note] Starting cufflinks step.

[Note] Starting cuffmerge step.

[Note] Starting cuffdiff step.

sh: R: command not found
Traceback (most recent call last):
  File "/data/users/dunnw/py273/bin/blacktie", line 8, in <module>
    load_entry_point('blacktie==0.2.1qf1', 'console_scripts', 'blacktie')()
  File "/data/users/dunnw/py273/lib/python2.7/site-packages/blacktie/scripts/blacktie_pipeline.py", line 236, in main
    from blacktie.scripts import cummerbund
  File "/data/users/dunnw/py273/lib/python2.7/site-packages/blacktie/scripts/cummerbund.py", line 37, in <module>
    raise errors.BlacktieError('Importing required module "rpy2" failed because no R application could be found on your system. Try again after instaling R.')
NameError: name 'errors' is not defined

Incorporate ruffus pipeline framework to better handle failed steps etc

Mac bug: pprocess AttributeError module object has no attribute 'poll'

Full traceback

Traceback (most recent call last):
  File "/Users/name/virtualPython/bin/blacktie", line 9, in
<module>
    load_entry_point('blacktie==0.2.1qf1', 'console_scripts', 'blacktie')()
  File
"/Users/name/virtualPython/lib/python2.7/site-packages/blacktie/scripts/blacktie_pipeline.py",
line 152, in main
    queue = pprocess.Queue(limit=yargs.cufflinks_options.p)
  File
"/Users/name/virtualPython/lib/python2.7/site-packages/pprocess.py",
line 806, in __init__
    Exchange.__init__(self, *args, **kw)
  File
"/Users/name/virtualPython/lib/python2.7/site-packages/pprocess.py",
line 277, in __init__
    self.poller = select.poll()
AttributeError: 'module' object has no attribute 'poll'

Adding PCA and MDS tests to cummerbund step

blacktie-cummerbund will soon run PCA, PCA-reps, MDS, and MDS-reps