BradnerLab/pipeline issues and pull requests

#82 - Installation failure of bamliquidator on centos7

Issue - State: open - Opened by Yuxuan0060 about 2 years ago

#81 - Restored bokeh plotting functionality with Docker build

Pull Request - State: open - Opened by jdimatteo almost 3 years ago

#80 - Installation failure in MacOS

Issue - State: open - Opened by xiaoyonf almost 4 years ago

#79 - bamliquidator_batch ValueError: cannot set WRITEABLE flag to True of this array

Issue - State: closed - Opened by raphaelbetschart almost 4 years ago - 1 comment

#78 - Adding docs from wiki to docs folder

Pull Request - State: closed - Opened by vsoch over 4 years ago

#77 - Quickly fix travis errors which seems to have been broken for years

Pull Request - State: closed - Opened by jdimatteo over 4 years ago - 1 comment

#76 - Adding instructions for build and usage of containers

Pull Request - State: closed - Opened by vsoch over 4 years ago - 7 comments

#75 - conversion from python2 to python3

Pull Request - State: closed - Opened by madetunj over 4 years ago

#74 - Add Python3 support

Pull Request - State: closed - Opened by jdimatteo almost 5 years ago

#73 - travis tests failing

Issue - State: open - Opened by jdimatteo almost 5 years ago - 1 comment

#72 - created a very simple test script for basic sanity after installation

Pull Request - State: closed - Opened by GodloveD almost 5 years ago - 2 comments

#71 - real examples with data and output

Issue - State: closed - Opened by GodloveD almost 5 years ago - 6 comments

#70 - Correct binsize calculation

Pull Request - State: open - Opened by Drmirdeep almost 5 years ago - 6 comments

#69 - Wrong binsize calculation accumulates offset errors with increasing bin numbers

Issue - State: open - Opened by Drmirdeep almost 5 years ago

#68 - Pypi packages are dropping python2 support

Issue - State: open - Opened by jvrakor almost 5 years ago

#67 - supported to run ROSE2 in python3 environment

Pull Request - State: open - Opened by gauravj49 about 5 years ago - 2 comments

#66 - support bionic for ppa

Pull Request - State: closed - Opened by jdimatteo over 5 years ago

#65 - networkScatter.R not found

Issue - State: closed - Opened by ssmadha almost 6 years ago - 2 comments

#64 - MAC installation problem

Issue - State: open - Opened by biogeeky almost 6 years ago

#63 - Docker

Pull Request - State: closed - Opened by jdimatteo almost 6 years ago - 5 comments

#62 - Operation Timed out on ROSE2

Issue - State: open - Opened by GryderArt over 6 years ago - 13 comments

#61 - bamliquidator_regions error

Issue - State: open - Opened by itsvenu over 6 years ago - 1 comment

#60 - Questions about installation and output

Issue - State: closed - Opened by datakid almost 7 years ago - 1 comment

#59 - Installation issue: -lbam is error, but hdf5/serial isn't a thing at all?

Issue - State: closed - Opened by datakid almost 7 years ago - 8 comments

#58 - Error in bamToGFF.py

Issue - State: closed - Opened by gunjangala about 7 years ago - 6 comments

#57 - bamliquidator: Installation issues

Issue - State: closed - Opened by itsvenu over 7 years ago - 6 comments

#56 - procedure to add a reference genome

Issue - State: closed - Opened by mpallocc over 7 years ago - 4 comments

#55 - Centos 6.8 build

Pull Request - State: closed - Opened by jdimatteo over 7 years ago

#54 - Motif liquidator matrix

Pull Request - State: closed - Opened by jdimatteo about 8 years ago

#53 - installation on MAC

Issue - State: closed - Opened by nbahlis almost 9 years ago - 9 comments

#52 - enable Jenkins motif liquidator tests on master branch when merged with master

Issue - State: open - Opened by jdimatteo almost 9 years ago - 1 comment

#51 - bamliquidator_batch now compatible with latest bokeh version

Pull Request - State: closed - Opened by jdimatteo about 9 years ago - 3 comments

#50 - global name 'maketrans' is not defined

Issue - State: closed - Opened by fburdet about 9 years ago - 3 comments

#49 - Unhandled exception: pthread_attr_setstacksize: Invalid argument

Issue - State: closed - Opened by davidhoover about 9 years ago - 7 comments

#48 - Reverted order of int casting to prevent divide by zero errors

Pull Request - State: closed - Opened by dpolaski about 9 years ago

#47 - Merged Fed's crc utils version with the current version

Pull Request - State: closed - Opened by dpolaski about 9 years ago

#46 - bamliquidator crashes after failed absurdly large memory allocation

Issue - State: closed - Opened by jdimatteo over 9 years ago - 3 comments
Labels: bug

#45 - consider using git submodules and allowing local builds of bamliquidator?

Issue - State: closed - Opened by semenko over 9 years ago - 5 comments

#44 - version 1.2 minor bug fixes and enhancements

Pull Request - State: closed - Opened by jdimatteo almost 10 years ago

#43 - bamliquidator_batch (calling bamliquidator_regions) fails on valid .bed file

Issue - State: closed - Opened by semenko almost 10 years ago - 4 comments
Labels: bug, pending-pull-request

#42 - provide option for a different normalization method

Issue - State: open - Opened by jdimatteo almost 10 years ago - 2 comments
Labels: enhancement

#41 - tod /crusader backup filesystem full

Issue - State: closed - Opened by jdimatteo almost 10 years ago - 7 comments

#40 - bamliquidator_batch -m option for multiple files should add columns

Issue - State: closed - Opened by jdimatteo almost 10 years ago
Labels: bug, pending-pull-request

#39 - Update Install Instructions when bamliquidator 1.2 released

Issue - State: closed - Opened by jdimatteo almost 10 years ago - 1 comment

#38 - clean up bamliquidator build and dput warnings

Issue - State: open - Opened by jdimatteo about 10 years ago
Labels: prio:low

#37 - consider adding an option to control the number of threads used by bamliquidator_batch

Issue - State: closed - Opened by jdimatteo about 10 years ago
Labels: enhancement, pending-pull-request

#36 - testing notifications

Issue - State: closed - Opened by bar2222 about 10 years ago

#35 - enhance reporting of parsing errors

Issue - State: open - Opened by jdimatteo about 10 years ago
Labels: enhancement

#34 - Exclude bad regions

Pull Request - State: closed - Opened by jdimatteo about 10 years ago - 2 comments

#33 - bamliquidator rounding error

Issue - State: closed - Opened by jdimatteo about 10 years ago - 3 comments
Labels: pending-pull-request

#32 - August 2014 bugs

Pull Request - State: closed - Opened by jdimatteo about 10 years ago - 1 comment

#31 - prevent out of sync versions for bamliquidator_batch / bamliquidator_bins / bamliquidator_regions

Issue - State: closed - Opened by jdimatteo about 10 years ago - 2 comments
Labels: enhancement, pending-pull-request

#30 - bamliquidator_region cannot handle non-canonical chromosome IDs

Issue - State: closed - Opened by jdimatteo about 10 years ago - 8 comments
Labels: bug, pending-pull-request

#29 - bamliquidator fails when bam files processed in current directory

Issue - State: closed - Opened by jdimatteo about 10 years ago
Labels: bug

#28 - bamliquidator upgrade instructions aren't working

Issue - State: closed - Opened by jdimatteo about 10 years ago - 1 comment

#27 - Logfile

Pull Request - State: closed - Opened by jdimatteo about 10 years ago - 11 comments

#26 - follow up on poor bokeh 0.5 performance

Issue - State: closed - Opened by jdimatteo about 10 years ago - 2 comments

#25 - samtools not installed by bamliquidator

Issue - State: closed - Opened by jdimatteo about 10 years ago

#24 - pdf loading time

Issue - State: open - Opened by huihuifan about 10 years ago

#23 - add version number to counts.h5 file

Issue - State: closed - Opened by jdimatteo over 10 years ago - 1 comment
Labels: enhancement, pending-pull-request

#22 - Long file names and specifying region format now supported

Pull Request - State: closed - Opened by jdimatteo over 10 years ago - 8 comments

#21 - Document/Test/Script bamliquidator_bach install with no admin rights

Issue - State: closed - Opened by jdimatteo over 10 years ago - 1 comment
Labels: enhancement, wontfix, prio:low

#20 - Zero region file error handling

Pull Request - State: closed - Opened by jdimatteo over 10 years ago

#19 - bamliquidator doesn't handle long file names

Issue - State: closed - Opened by jdimatteo over 10 years ago
Labels: bug, pending-pull-request

#18 - bamliquidator verbose output and logging

Issue - State: closed - Opened by jdimatteo over 10 years ago - 7 comments
Labels: enhancement, pending-pull-request

#17 - bamliquidator_batch "UserWarning: Installed openpyxl is not supported"

Issue - State: closed - Opened by jdimatteo over 10 years ago
Labels: bug, prio:low

#16 - bamliquidator_regions should accept other file extensions

Issue - State: closed - Opened by semenko over 10 years ago - 1 comment
Labels: pending-pull-request

#15 - bamliquidator_regions should better handle a zero region file

Issue - State: closed - Opened by jdimatteo over 10 years ago - 1 comment
Labels: bug, pending-pull-request

#14 - Ease Installation

Pull Request - State: closed - Opened by jdimatteo over 10 years ago - 1 comment

#13 - bamliquidator should support outputting files into an existing directory

Issue - State: closed - Opened by jdimatteo over 10 years ago

#12 - fixed uninitialized garbage values when error occurred during liquidation

Pull Request - State: closed - Opened by jdimatteo over 10 years ago