ComparativeGenomicsToolkit/hal issues and pull requests

#214 - Specify phast commit in README

Pull Request - State: closed - Opened by glennhickey over 3 years ago

#213 - How to get output URL for hal2assemblyHub.py?

Issue - State: open - Opened by Solenyalyl over 3 years ago - 3 comments

#212 - Support large numbers of children

Issue - State: closed - Opened by glennhickey over 3 years ago - 14 comments

#211 - HAL doesn't compile

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

#210 - HAL Replacegenome failed halValidate

Issue - State: open - Opened by EdYSChuang815 almost 4 years ago

#209 - UCSC genome browser fails to display an assembly hub due to a hal get blocks error

Issue - State: open - Opened by ybukhman almost 4 years ago - 1 comment

#208 - halReplaceGenome error

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

#207 - hal2mafMP.py doesn't find sonLib

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

#206 - Poke CI

Pull Request - State: closed - Opened by glennhickey almost 4 years ago

#205 - installation problem

Issue - State: closed - Opened by Tkastylevsky almost 4 years ago - 3 comments

#204 - fixed bug where openGenomeCheck had been not correctly being changed …

Pull Request - State: closed - Opened by diekhans almost 4 years ago

#203 - HalPhyloPTrain.py error

Issue - State: open - Opened by SimonaSecomandi almost 4 years ago - 4 comments

#202 - hal2maf Segmentation fault

Issue - State: open - Opened by lwlive almost 4 years ago - 6 comments
Labels: bug

#201 - halPhyloPTrain.py on ancestral repeats for halPhyloPMP.py

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

#200 - Remve singleMachine batch system check from hal2assemblyHub.py

Pull Request - State: closed - Opened by glennhickey almost 4 years ago

#199 - RuntimeError: singleMachine is the only supported batchSystem

Issue - State: open - Opened by saoirseguita almost 4 years ago - 3 comments

#198 - Path / directory structure errors

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

#197 - halPhyloPTrain.py with ancestral repeats

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

#196 - installation issue: fit_column.h

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

#195 - hal2mafMP.py error: Invalid range specified for convertGenome

Issue - State: open - Opened by anecsulea almost 4 years ago - 6 comments

#194 - halSnps conversion problem

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

#193 - hal2chain for faster halLiftover

Issue - State: open - Opened by badoi almost 4 years ago - 5 comments

#192 - parsing .hal file by list of species

Issue - State: open - Opened by devonorourke about 4 years ago - 5 comments

#191 - bed file used in hal4dextract

Issue - State: open - Opened by biozhangzhou about 4 years ago

#190 - Is it possible to get all the pairwise mapping position by hal2paf?

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

#189 - hal2maf export score

Issue - State: open - Opened by zhenzhenyang-psu about 4 years ago

#188 - hal2assemblyHub.py Invalid tree error when computing conservation tracks

Issue - State: closed - Opened by alexgilgal about 4 years ago - 1 comment

#187 - The results of halTreePhyloP.py

Issue - State: open - Opened by minjinhan about 4 years ago

#186 - HDF5 error with hal2maf after using halReplaceGenome

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

#185 - fixed compatiblity with various versions of HDF5 and recent changes to kent library

Pull Request - State: closed - Opened by diekhans about 4 years ago

#184 - halPhyloPTrain error

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

#183 - Getting Chromosome Sizes from hal File

Issue - State: closed - Opened by imk1 about 4 years ago - 2 comments

#182 - correctly return error if halOpenHalOrLod() is done on a non-existant file

Pull Request - State: closed - Opened by diekhans about 4 years ago

#180 - Fixed compile errors with that have crept in with optional UDC cache

Pull Request - State: closed - Opened by diekhans about 4 years ago

#177 - hal2maf should add maf header

Issue - State: closed - Opened by diekhans about 4 years ago - 1 comment

#173 - UDC support no longer compiles

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

#159 - halSnps segfaults on many inputs

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

#142 - make: *** [../rules.mk:32: ../bin/halApiTests] Error 1

Issue - State: open - Opened by Boer223 over 4 years ago - 4 comments

#129 - hal2mafMP.py modulenotfounderror sonLib.bioio

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

#117 - --splitBySequence, --refTargets or --refSequence required

Issue - State: closed - Opened by fenderglass almost 5 years ago - 8 comments

#115 - halCoverage crashes on invalid genome name

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

#83 - make[1]: *** [../objs/phyloP/impl/halPhyloPMain.o] Error 1

Issue - State: closed - Opened by shameem356 over 5 years ago - 13 comments

#78 - Make error for hal : /bin/sh: 1: h5c++: not found

Issue - State: closed - Opened by krostifangers almost 6 years ago - 4 comments

GitHub / ComparativeGenomicsToolkit/hal issues and pull requests