biocore/burrito-fillings issues and pull requests

#74 - update to swarm 2

Issue - State: open - Opened by colinbrislawn over 8 years ago - 1 comment

#73 - added thread parameter to mafft

Pull Request - State: closed - Opened by ekopylova over 8 years ago - 1 comment

#72 - output .uc file with root file name of output filepath

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

#71 - Mothur app controller fails when temp directory has dash in filepath

Issue - State: open - Opened by kylebittinger about 9 years ago

#70 - updated usearch.py to properly suppress chimera checking

Pull Request - State: open - Opened by colinbrislawn about 9 years ago

#69 - REL/MAINT: update for 0.1.1-dev, add cogent dependency

Pull Request - State: closed - Opened by gregcaporaso over 9 years ago

#68 - 0.1.1 release

Pull Request - State: closed - Opened by gregcaporaso over 9 years ago

#67 - fix biocore/qiime#2007

Pull Request - State: closed - Opened by antgonza over 9 years ago - 4 comments

#66 - fixes qiime issue 2014

Pull Request - State: closed - Opened by antgonza over 9 years ago - 2 comments

#65 - cleaned up usage of /tmp in application controllers most frequently used by QIIME

Pull Request - State: closed - Opened by gregcaporaso over 9 years ago

#64 - clean-up usage of "/tmp" for fillings most frequently used by QIIME

Issue - State: closed - Opened by gregcaporaso over 9 years ago - 2 comments

#63 - added version to init.py

Pull Request - State: closed - Opened by gregcaporaso over 9 years ago - 1 comment

#62 - grep the burrito-fillings code base for /tmp and replace with tempfile.gettempdir()

Issue - State: open - Opened by gregcaporaso over 9 years ago

#61 - Mothur tmpfiles

Pull Request - State: closed - Opened by kylebittinger over 9 years ago - 5 comments

#60 - Fix test failure due to extra whitespace in mothur taxonomy summary.

Pull Request - State: closed - Opened by kylebittinger over 9 years ago - 1 comment

#59 - cleaned and updated Mafft controller

Pull Request - State: closed - Opened by RNAer over 9 years ago - 9 comments

#58 - HMMER app controller (specifically for command nhmmer)

Pull Request - State: open - Opened by ekopylova over 9 years ago

#57 - VSEARCH app controller

Pull Request - State: closed - Opened by ekopylova over 9 years ago - 9 comments

#56 - improve uclust application controller error reporting

Issue - State: open - Opened by ebolyen almost 10 years ago

#55 - uclust.py should accept a temporary directory as an argument

Issue - State: open - Opened by ebolyen almost 10 years ago - 2 comments

#54 - burrito-fillings is missing version

Issue - State: closed - Opened by jairideout almost 10 years ago - 4 comments

#53 - Add option to change base name of sortmerna's output files

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

#52 - updated version string for 0.1.0 development cycle

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

#51 - 0.1.0 release candidate

Pull Request - State: closed - Opened by gregcaporaso almost 10 years ago - 1 comment

#50 - package rename

Pull Request - State: closed - Opened by gregcaporaso almost 10 years ago - 1 comment

#49 - change name of brokit and do a 0.1.0 release

Issue - State: closed - Opened by gregcaporaso almost 10 years ago - 3 comments
Labels: question

#48 - updates to skbio 0.2.1

Pull Request - State: closed - Opened by gregcaporaso almost 10 years ago - 8 comments

#47 - update to skbio 0.2.1

Issue - State: closed - Opened by gregcaporaso almost 10 years ago

#46 - resolves issue https://github.com/biocore/brokit/issues/45

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

#45 - usearch de novo (no chimera checking) gives incorrect results

Issue - State: open - Opened by ekopylova almost 10 years ago

#44 - App controller for sortmerna mapper

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

#43 - Import from burrito

Pull Request - State: closed - Opened by jairideout about 10 years ago

#42 - Update sumaclust tests

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

#41 - Add API + tests for Swarm

Pull Request - State: closed - Opened by ekopylova about 10 years ago - 5 comments

#40 - updates for transition from skbio to burrito for application controller framework

Issue - State: closed - Opened by gregcaporaso about 10 years ago - 6 comments

#39 - ENH: updated skbio dependency, fixes #38

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

#38 - update to use skbio 0.1.4

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

#37 - update to sortmerna api

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

#36 - add import of cogent aligner for access in QIIME

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

#35 - remove tmp dir and close(f)

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

#34 - Change to the numpy doc standard for sortmerna + sumaclust api's

Issue - State: open - Opened by ekopylova over 10 years ago

#33 - App controller for SumaClust v1.0

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

#32 - Sortmerna api

Pull Request - State: closed - Opened by ekopylova over 10 years ago - 3 comments

#31 - brokit.get_clusters_from_fasta_filepath failing to remove output files

Issue - State: open - Opened by charudatta-navare over 10 years ago - 1 comment

#30 - Vienna package controller

Issue - State: open - Opened by squirrelo over 10 years ago

#29 - Update to skbio 0.1.1

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

#28 - adding an import that the denoiser needs

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

#27 - update brokit license information to indicate that it's actually GPL

Issue - State: open - Opened by gregcaporaso over 10 years ago - 1 comment

#26 - updated imports

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

#25 - not a hack

Pull Request - State: closed - Opened by gregcaporaso over 10 years ago - 6 comments

#24 - added an import so we can access it from QIIME

Pull Request - State: closed - Opened by gregcaporaso over 10 years ago - 2 comments

#23 - added default moltype for infernal

Pull Request - State: closed - Opened by gregcaporaso over 10 years ago - 9 comments

#22 - Allow for `--usearch_local` in usearch 6.1

Issue - State: open - Opened by audy over 10 years ago - 1 comment

#21 - missing tmp dir in get_clusters_from_fasta_filepath function from uclust

Issue - State: open - Opened by josenavas over 10 years ago

#20 - brokit-wrapped applications that are not currently installed in the QIIME VM

Issue - State: open - Opened by gregcaporaso over 10 years ago - 7 comments

#19 - modified to define default moltype for functions used in QIIME

Pull Request - State: closed - Opened by gregcaporaso over 10 years ago - 16 comments

#18 - Fix import statements

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

#17 - brokit changes to help remove cogent dependency from qiime

Issue - State: closed - Opened by gregcaporaso over 10 years ago - 3 comments

#16 - imports from skbio.parse.fasta

Issue - State: closed - Opened by wasade over 10 years ago - 3 comments

#15 - Fixing fasta parser imports

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

#14 - Changing skbio.parse.fasta to skbio.parse.sequences

Pull Request - State: closed - Opened by josenavas over 10 years ago - 5 comments

#13 - Porting all the app controllers that QIIME imports from cogent

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

#12 - Adding COPYING files and editing README.md

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

#11 - Porting cd-hit app controller

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

#10 - Porting rtax app controller

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

#9 - Porting formatdb and blast app controllers

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

#8 - Porting the infernal application controller

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

#7 - Add brokit acronym to README.md

Issue - State: closed - Opened by jairideout over 10 years ago - 1 comment
Labels: enhancement

#6 - Porting Pycogent backports

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

#5 - mothur.py app controller may not be completely tested

Issue - State: open - Opened by josenavas over 10 years ago

#4 - rdp_classifier.py app controler may not include complete tests

Issue - State: open - Opened by josenavas over 10 years ago

#3 - seqprep.py app controller does not have tests

Issue - State: open - Opened by josenavas over 10 years ago - 1 comment

#2 - fastq_join.py app controller does not have tests

Issue - State: open - Opened by josenavas over 10 years ago - 2 comments

#1 - Which application controllers do we want to maintain?

Issue - State: open - Opened by josenavas over 10 years ago - 9 comments

GitHub / biocore/burrito-fillings issues and pull requests