smirarab/pasta issues and pull requests

#64 - problem with pasta

Issue - State: open - Opened by ChaoShenzjs over 1 year ago - 1 comment

#63 - Failed to run hmmeralign

Issue - State: open - Opened by marinamashintsova over 1 year ago

#62 - Unsupported operand types with guide tree

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

#61 - Continue crashed analysis from tree inference step

Issue - State: open - Opened by diegomarquezp about 3 years ago - 8 comments

#60 - Crashed in tree building step

Issue - State: closed - Opened by diegomarquezp over 3 years ago - 2 comments

#59 - soft link dependency locations in conda build script

Pull Request - State: closed - Opened by krinsman over 3 years ago - 1 comment

#58 - ValueError: The alignment file has no sequences. PASTA quits.

Issue - State: closed - Opened by srautonu over 3 years ago - 1 comment

#57 - Issue running default settings

Issue - State: closed - Opened by antoinekoehl over 3 years ago - 5 comments

#56 - Docker not working with MUSCLE aligner

Issue - State: open - Opened by A-Swafford almost 4 years ago - 2 comments

#55 - Terminated abnormally

Issue - State: closed - Opened by lalalagartija about 4 years ago - 2 comments

#54 - GUI error: Bad CPU type in executable

Issue - State: open - Opened by pwkooij about 4 years ago - 12 comments

#53 - GUI does not start the alignment

Issue - State: closed - Opened by golgicik over 4 years ago - 1 comment

#52 - Why aren't Saté & Pasta listed in the "External Tools" aligners?

Issue - State: open - Opened by hhg7 over 4 years ago - 1 comment

#51 - Job is taking too much time for insitutional HPC and has poor CPU efficiency

Issue - State: closed - Opened by clb21565 over 4 years ago - 4 comments

#50 - TreeShrink error

Issue - State: open - Opened by sjfleck over 4 years ago - 8 comments

#49 - Pasta fails with no error, job just disappears

Issue - State: closed - Opened by hhg7 over 4 years ago - 4 comments

#48 - Pasta fails with homologs and muscle -> no sequences

Issue - State: open - Opened by hhg7 over 4 years ago - 4 comments

#47 - Update README.md

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

#46 - readme linux/mac instructions are swapped

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

#45 - Update README

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

#44 - GINSI appears to be missing from binary bundle

Issue - State: closed - Opened by brantfaircloth about 5 years ago - 1 comment

#43 - update Docker file for java

Pull Request - State: closed - Opened by smirarab about 5 years ago

#42 - Conda

Pull Request - State: closed - Opened by smirarab about 5 years ago

#41 - Better describe the --treeshrink-filter option

Issue - State: open - Opened by smirarab about 5 years ago

#40 - Bioconductor install doesn't work

Issue - State: open - Opened by brendanf over 5 years ago - 1 comment

#39 - error on identical alignments

Issue - State: closed - Opened by B10KGenomes over 5 years ago - 1 comment

#38 - small issue with run_pasta_gui.py and run_pasta.py -h or -i options.

Issue - State: closed - Opened by kibet-gilbert over 5 years ago - 2 comments

#37 - Error opal.jar

Issue - State: closed - Opened by sumoumouElin almost 6 years ago - 10 comments

#36 - GUI unable to setup configuration file

Issue - State: closed - Opened by NElnour almost 6 years ago - 9 comments

#35 - --num_cpus didn't work for me

Issue - State: closed - Opened by mcsimenc over 6 years ago - 2 comments

#34 - added checks in setup.py and made it compatible with python 3

Pull Request - State: closed - Opened by koditaraszka over 6 years ago

#33 - Added Dockerfile

Pull Request - State: closed - Opened by niemasd over 6 years ago

#32 - Docker image instead of VM

Issue - State: closed - Opened by niemasd over 6 years ago - 3 comments
Labels: enhancement

#31 - Fixed tab/space issue in setup.py

Pull Request - State: closed - Opened by niemasd over 6 years ago

#30 - Issues in setup.py

Issue - State: open - Opened by niemasd over 6 years ago - 10 comments

#29 - Update README.md

Pull Request - State: closed - Opened by koditaraszka over 6 years ago

#28 - new sub-aligners within PASTA

Pull Request - State: closed - Opened by koditaraszka over 6 years ago

#27 - init_aln is not registered as a temporary directory that was created by this process

Issue - State: open - Opened by jpearl01 over 6 years ago

#26 - Using logging system everywhere

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

#25 - extra ;

Issue - State: closed - Opened by smirarab almost 7 years ago

#24 - Fixed bug in mincluster

Pull Request - State: closed - Opened by uym2 almost 7 years ago

#23 - remove the problematic commit

Pull Request - State: closed - Opened by uym2 almost 7 years ago

#22 - New decomposition: minimum clustering

Pull Request - State: closed - Opened by uym2 almost 7 years ago

#21 - update settings.py, tools.py, and setup.py

Pull Request - State: closed - Opened by koditaraszka about 7 years ago

#20 - obvious misalignments

Issue - State: closed - Opened by pwkooij about 7 years ago - 1 comment

#19 - fix formatting and typos

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

#18 - Spawning multiple threads causes segfault or BlockingIOError

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

#17 - Pasta installation requires gcc version 2.14 on Linux

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

#16 - Python 3 compatibility

Issue - State: closed - Opened by niemasd almost 8 years ago

#15 - Ported to DendroPy 4

Pull Request - State: closed - Opened by niemasd almost 8 years ago

#14 - Ported to Dendropy 4

Pull Request - State: closed - Opened by niemasd almost 8 years ago

#13 - Is PASTA CUDA-enabled?

Issue - State: closed - Opened by Pejvak1 almost 8 years ago - 4 comments

#12 - Is PASTA CUDA-enabled?

Issue - State: closed - Opened by Pejvak1 almost 8 years ago

#11 - Is PASTA CUDA-enabled?

Issue - State: closed - Opened by Pejvak1 almost 8 years ago

#10 - undefined variable in alignment.py

Issue - State: closed - Opened by joelarmstrong about 10 years ago - 1 comment
Labels: bug

#9 - Provide the merging machinery as an stand-alone app

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

#8 - GUI sometimes refuses to start a new job when the old one is prematurely stopped.

Issue - State: open - Opened by smirarab about 10 years ago
Labels: bug

#7 - Error reporting and catching

Issue - State: closed - Opened by smirarab about 10 years ago - 1 comment
Labels: bug

#6 - Add a script for masking and converting alignment formats

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

#5 - mask initial alignment from hmmer based on insertion columns.

Issue - State: open - Opened by smirarab over 10 years ago
Labels: enhancement

#4 - use multiple cpus for initial alignment

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

#3 - masking does not work for raxml

Issue - State: closed - Opened by smirarab over 10 years ago
Labels: bug

#2 - masking does not work for raxml

Issue - State: closed - Opened by smirarab over 10 years ago
Labels: duplicate

#1 - Model field for FastTree in config file not being properly set

Issue - State: closed - Opened by namphuon over 10 years ago - 1 comment
Labels: bug

GitHub / smirarab/pasta issues and pull requests