annocomba v0.1.2

Changes since last release:
53baa15 bump version to 0.1.2
ecbabd1 More sensitive time settings for vsc5 configfile
1471d22 Improve handling of transcript evidence files. Hopefully correct now.
aa7851d Add GitHub workflow to create automated releases
4d222b2 Fix conflicting options string error with --tmpdir
5facb8c Add flag so that tmp direcory for shadow files can be used
5206c42 Fix import of snakefiles to remove depedency issue
73044d3 Add preliminary functionality to identify TEs with EDTA
cc2ab86 Rename annotate Snakefile
f3f695a Split call-genes and annotate snakefile
13066b2 Remove premature exit after interproscan setup
55cf467 Fix typo in funannotate setup
01c58cb Check for successful repeatmasker setup before adding bindpoint to avoid error during maker setup
18ad630 Improve output of annocomba setup including some checks if all required files are present
7d08c2c Fix indentation error
32ecf0c Create funannotate database during setup if it does not exist
d0a32d8 Interproscan path change in rule
9984234 Make interproscan setup more general
eda0c84 Add check-setup util plus some usage-infos
070ab30 bump version to 0.1.1
1b87f46 Fix small error in setup_eggnog
69ff04d Use input rule to determine which functional annotations should be produced. Code cleanups in annocomba script
33bca3e Increase RAM for AUGUSTUS_PASS2 rule
1f98307 Update README
6c04ec2 Modify functional annotation rules to match new wildcard scheme and --select
ce4fd07 Rename funannotate_predict rulefile
79828e7 Remove some old files
cfa48b1 Add missing python script to manage jobs
81be216 Improve behavior for --select slightly
bee86bd Add --select to subset analyzed samples. Clean up wildcards in funannotate predict. Fix Augustus config path issue in funannotate predict
3998206 Add VSC% cluster config file
1a21721 Improve handling of EST evidence files
4edc963 Add basic checks for config files
a422e77 Make annocomba.py annocomba
c511e1a Add funannotate-remote and eggnog functionality to annotate. Clean up some rules and fix split_proteins rule
3c420ec Add basic functionality to predict functions with interproscan
d7d90e7 Increase verbosity and add additional checks to handling of EST evidence files
3a57688 Add conversion of multiple Interproscan XMLs to final rule of iprscan functionality
cb8772b Improved handling of EST evidence. This can now also be done in the samples TSV file
ebf1b5b Add parallel interproscan rule and basic functional annotations
34a3e57 Add aggregate_funannotate_predict rule
df1a0ba Fix logging of funannotate predict
f634e1e Fix some wrong paths in new funannotate predict rule
e1aff03 Basic handling of different gene-call combinations. Update gsc cluster config file
1c42e23 First work on gene prediction with funannotate predict
04d955f Fix Bug in how Genemark bindpoint is set during setup
87a61a7 Add some checks to annocomba script for python modules
b586e49 Fix setup_maker rule again
5ab4a23 Comment out funannotate rules from maker all rule
4133b25 Correct rule file paths
28baef1 Add extended error handling for cases where maker or repbase tarballs don't exist
83df4a2 Fix container location for setup funannotate
609f216 Add basic util functionality. Split runmodes into gene calling and annotation steps
99ba53f Add immediate-submit submodule
f4c5812 Basic setup functionality finished
326ba82 Initial commit to transition to python based annocomba script. First improvements to setup step

annocomba v0.1.1

Changes since last release:
ecbabd1 More sensitive time settings for vsc5 configfile
1471d22 Improve handling of transcript evidence files. Hopefully correct now.
aa7851d Add GitHub workflow to create automated releases
4d222b2 Fix conflicting options string error with --tmpdir
5facb8c Add flag so that tmp direcory for shadow files can be used
5206c42 Fix import of snakefiles to remove depedency issue
73044d3 Add preliminary functionality to identify TEs with EDTA
cc2ab86 Rename annotate Snakefile
f3f695a Split call-genes and annotate snakefile
13066b2 Remove premature exit after interproscan setup
55cf467 Fix typo in funannotate setup
01c58cb Check for successful repeatmasker setup before adding bindpoint to avoid error during maker setup
18ad630 Improve output of annocomba setup including some checks if all required files are present
7d08c2c Fix indentation error
32ecf0c Create funannotate database during setup if it does not exist
d0a32d8 Interproscan path change in rule
9984234 Make interproscan setup more general
eda0c84 Add check-setup util plus some usage-infos
070ab30 bump version to 0.1.1
1b87f46 Fix small error in setup_eggnog
69ff04d Use input rule to determine which functional annotations should be produced. Code cleanups in annocomba script
33bca3e Increase RAM for AUGUSTUS_PASS2 rule
1f98307 Update README
6c04ec2 Modify functional annotation rules to match new wildcard scheme and --select
ce4fd07 Rename funannotate_predict rulefile
79828e7 Remove some old files
cfa48b1 Add missing python script to manage jobs
81be216 Improve behavior for --select slightly
bee86bd Add --select to subset analyzed samples. Clean up wildcards in funannotate predict. Fix Augustus config path issue in funannotate predict
3998206 Add VSC% cluster config file
1a21721 Improve handling of EST evidence files
4edc963 Add basic checks for config files
a422e77 Make annocomba.py annocomba
c511e1a Add funannotate-remote and eggnog functionality to annotate. Clean up some rules and fix split_proteins rule
3c420ec Add basic functionality to predict functions with interproscan
d7d90e7 Increase verbosity and add additional checks to handling of EST evidence files
3a57688 Add conversion of multiple Interproscan XMLs to final rule of iprscan functionality
cb8772b Improved handling of EST evidence. This can now also be done in the samples TSV file
ebf1b5b Add parallel interproscan rule and basic functional annotations
34a3e57 Add aggregate_funannotate_predict rule
df1a0ba Fix logging of funannotate predict
f634e1e Fix some wrong paths in new funannotate predict rule
e1aff03 Basic handling of different gene-call combinations. Update gsc cluster config file
1c42e23 First work on gene prediction with funannotate predict
04d955f Fix Bug in how Genemark bindpoint is set during setup
87a61a7 Add some checks to annocomba script for python modules
b586e49 Fix setup_maker rule again
5ab4a23 Comment out funannotate rules from maker all rule
4133b25 Correct rule file paths
28baef1 Add extended error handling for cases where maker or repbase tarballs don't exist
83df4a2 Fix container location for setup funannotate
609f216 Add basic util functionality. Split runmodes into gene calling and annotation steps
99ba53f Add immediate-submit submodule
f4c5812 Basic setup functionality finished
326ba82 Initial commit to transition to python based annocomba script. First improvements to setup step

annocomba original

This is a backup of the original annocomba pipeline before the first large overhaul.