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Releases: eead-csic-compbio/get_homologues

get_homologues-est

07 Aug 15:57
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This release includes the following updates:

updated BLAST to ncbi-blast-2.16.0+ binaries
test_get_homologues.t now can actually download 8 genomes from NCBI
test_get_homologues.t now includes get_homologues.pl -X (diamond)
improved repository README.md with TOC and links to sections

binaries

07 Aug 14:39
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Compressed TAR file with binaries to be downloaded after cloning the source repository. This should be done with install.pl

Updated NCBI BLAST+ 2.16.0

get_homologues-est

13 Jun 07:30
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This release includes the following updates:

  • removed .gbk files from test_Streptococcus, should make releases smaller
  • added test_Streptococcus and HOWTOTettelin.txt to repo, only in releases before
  • updated manuals

get_homologues-est

07 Nov 10:40
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This release includes the following updates:

  • added new script MSA_Ka_Ks.pl to user_utils/dNdS
  • added target 'test nonet' to Makefile to allow tests in servers with closed ports
  • added parse_pangenome_matrix.pl -R, which modifies -P to control %PAV only for -B
  • phyTools::same_sequence_order checks for internal STOP codons in translated sequences
  • annotate_cluster.pl fails gracefully when no sequences are read
  • annotate_cluster.pl -b -P prints total missense mutations instead of SNPS

get_homologues-est

15 May 13:19
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This release ships with several changes and fixes:

15052023: updated BLAST to faster, smaller ncbi-blast-2.14.0+ binaries
15052022: update install.pl and updated bin.tgz (v3.6)

binaries

15 May 13:00
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Compressed TAR file with binaries to be downloaded after cloning the source repository. This should be done with install.pl

Updated NCBI BLAST+ 2.14.0

get_homologues-est

05 May 11:28
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This release ships with several changes and fixes:

07122022: compare_clusters.pl can intersect clusters from get_pangenes.pl
10032023: check_BDBHs.pl now guesses -i strings literally, escaping special chars
17032023: Release 22-282 of mcl is available, "but MCL itself is unchanged", we'll keep using mcl-14-137
22032023: annotate_cluster.pl -u produces unaligned complete sequences, flipped if required to facilitate multiple alignments
28032023: added more dependencies required for compiling R packages in install_R_deps.R
05052023: check that download_genomes_ncbi.pl still works with sample_genome.list

get_homologues-est

22 Aug 10:50
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This release ships with several changes and fixes:

10062022: annotate_cluster.pl -D can now annotate Pfam domains of singleton clusters
10062022: updated .travis.yaml (perl 5.32, libdb-dev, do not apt update)
14062022: compare_clusters.pl can read .cluster_list files from get_pangenes.pl
15062022: added sub same_sequence_order to lib/phyTools.pm
15062022: get_homologues-est.pl now checks that CDS .fna & .faa sequences are in same order
22082022: when checking that .fna & .faa sequences are in same order, CDSs with Ns are skipped
22082022: updated manual-est with description of pangenome matrix versions taken from tutorial

get_homologues-est

16 May 13:43
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This is the first release after publishing GET_HOMOLOGUES and GET_HOMOLOGUES-EST in bioconda

get_homologues-est

29 Apr 10:45
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This release ships with several changes and fixes:

20042022: added parse_pangenome_matrix.pl -n for matrices that do not include cloud clusters
21042022: transcripts2cdsCPP.pl not tested by default with make test, as bioconda lacks Inline::CPP
21042022: if bin/ not in place phyTools::set_phyTools_env assumes binary dependencies in PATH
21042022: updated install.pl so that it copes with binary dependencies in PATH
21042022: install.pl no_databases COGS only gets/compiles COGS, so that other binaries can be taken from PATH
22042022: added CODE_OF_CONDUCT
28042022: added test_swiss to Makefile
28042022: added compila_conda.pl to bin/COGsoft & added $(CXX) to Makefiles to use in conda recipe (macosx-intel copy still the same)
28042022: COGsoft source released as https://github.com/eead-csic-compbio/get_homologues/releases/download/v3.4.6/COGsoft.tgz
28042022: released updated bin.tgz (v3.5)