mattb112885 clusterDbAnalysis issues

mattb112885 / clusterDbAnalysis

ITEP - Integrated Toolkit for Exploration of microbial Pan-genomes

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issues

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Error in setup_step1.sh

#83 mbeasier closed 5 years ago
4
Using my own data from JGI

#82 marciomagrini closed 6 years ago
3
Error in convertGenbank2table.py if /pseudo in genbank

#81 michoug opened 7 years ago
5
Updating from ETE2 to ETE3

#80 JosephRyanPeterson opened 7 years ago
5
Python 3 support

#79 JosephRyanPeterson closed 7 years ago
0
Ported ITEP to Python 3

#78 JosephRyanPeterson closed 7 years ago
0
Feature request: Ability to run convertGenbank2table.py on multiple genomes

#77 ninjatacoshell closed 8 years ago
4
SQLite3 error: database or disk is full and no such table: main.blastnres_selfbit

#76 cvn001 closed 8 years ago
7
Error with rpsblast

#75 mkroege1 closed 8 years ago
1
Problem with gbk using convertGenbank2table.py

#74 FelipeMelis closed 8 years ago
3
sqlite3 in setup_step1.sh incredibly slow

#73 jnesme closed 7 years ago
3
sqlite3.OperationalError

#72 spaver opened 8 years ago
3
Apparent Issue with rerunning mcl

#71 jbird9 closed 8 years ago
4
Error in gene neighborhoods

#70 leoliuzhenshan opened 8 years ago
5
Error in ./convertGenbank2table.py

#69 meileel closed 8 years ago
6
Experimental ui

#68 BrunoWeiss opened 8 years ago
1
Error (?) using setup_step1.sh

#67 qu4drupole closed 8 years ago
2
Contig names are incorrect for genbank files with multiple contigs [Regression]

#66 mattb112885 closed 10 years ago
0
Error with the creation of CDD database

#65 Greg568 closed 8 years ago
1
Clarification of terms for mcl

#64 jcthrash closed 10 years ago
2
Unknown error running setup_step4.sh

#63 jcthrash closed 10 years ago
5
Improve neighborhood getting for tblastn hits

#62 mattb112885 opened 10 years ago
0
generateOrganismFileFromGbk.sh not running

#61 jcthrash closed 10 years ago
11
convertGenbank2table.py not running to completion with IMG-generated genbank files

#60 jcthrash closed 10 years ago
6
Genbank file issues with spliced proteins

#59 nick-youngblut opened 10 years ago
5
FastTree missing from VM

#58 mattb112885 opened 10 years ago
0
Sanitized gene IDs do not work with db_displayTree or db_replaceGeneWithAnnotation

#57 mattb112885 closed 10 years ago
1
orthomcl wrapper singleton issue

#56 mattb112885 opened 10 years ago
0
Using version numbers different from existing PubSEED version numbers fails

#55 mattb112885 closed 10 years ago
1
There is no function to get description \name for a cluster ID

#54 mattb112885 closed 11 years ago
1
Add gene IDs to genbank files

#53 mattb112885 closed 11 years ago
1
Issue with contig order from Biopython?

#52 mattb112885 closed 11 years ago
1
Need to build a 64-bit version of the VM

#51 mattb112885 closed 10 years ago
1
get_RAST_jobs.pl -h prints to std error, not std out

#50 JamesRH closed 11 years ago
1
James rh commits

#49 JamesRH closed 11 years ago
2
Change file input and output from sanatised organism name to (sanatized) organism ID

#48 JamesRH opened 11 years ago
3
Global bootstrapping defaults for FastTree_wrapper.py

#47 JamesRH closed 11 years ago
1
env variable for FastTree_wrapper.py to set number of cores

#46 JamesRH closed 11 years ago
1
Building RPSBLAST databases no longer works with current CDD data

#45 mattb112885 closed 11 years ago
4
Change database declarations into SQLite standard types

#44 mattb112885 closed 11 years ago
1
Bidirectional-best hits script should include the option to filter by organisms or genes

#43 mattb112885 closed 10 years ago
1
Make BLAST E-value cutoff a parameter to main.sh

#42 mattb112885 closed 11 years ago
1
Documentation for table headers

#41 JamesRH closed 11 years ago
1
Need a function to reroot a tree without replacing gene names with organism names and annotations

#40 mattb112885 closed 11 years ago
1
change SourceMe so people don't run it and not have the right PATH set

#39 JamesRH closed 11 years ago
1
Remove references to organism abbreviations in the organisms file

#38 mattb112885 closed 11 years ago
1
Remove old implicit shell script calls and replace with library functions

#37 mattb112885 opened 11 years ago
0
Need to move other things that make up their own scoring schemes to the standard library functions

#36 mattb112885 opened 11 years ago
0
convertGenbankToTable needs to check for taxID consistency in concatinated genbank file

#35 mattb112885 opened 11 years ago
1
Presence and absence relative to tree neighbors (instead of whole tree)

#34 mattb112885 closed 10 years ago
1