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freebsd-ports/biology
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Stefan Eßer bcaf25a8c8 Fix CONFLICTS entries of multiple ports 
There have been lots of missing CONFLICTS_INSTALL entries, either
because conflicting ports were added without updating existing ports,
due to name changes of generated packages, due to mis-understanding
the format and semantics of the conflicts entries, or just due to
typoes in package names.

This patch is the result of a comparison of all files contained in
the official packages with each other. This comparison was based on
packages built with default options and may therefore have missed
further conflicts with optionally installed files.

Where possible, version numbers in conflicts entries have been
generalized, some times taking advantage of the fact that a port
cannot conflict with itself (due to logic in bsd.port.mk that
supresses the pattern match result in that case).

A few ports that set the conflicts variables depending on complex
conditions (e.g. port options), have been left unmodified, despite
probably containing outdated package names.

These changes should only affect the installation of locally built
ports, not the package building with poudriere. They should give an
early indication of the install conflict in cases where currently
the pkg command aborts an installation when it detects that an
existing file would be overwritten,

Approved by:	portmgr (implicit)
2022-01-10 16:15:39 +01:00
..
abyss cleanup: drop support for EOL FreeBSD 11.X 2021-09-30 23:23:30 +02:00
ad2vcf biology/ad2vcf: Update to 0.1.4 2021-12-14 13:45:31 -06:00
artemis
avida
babel */*: Remove redundant '-*' from CONFLICTS definitions 2021-11-25 22:40:11 +01:00
bamtools devel/jsoncpp: Update to 1.9.4 -> 1.9.5 2021-11-05 12:09:19 -07:00
bamutil Fix CONFLICTS entries of multiple ports 2022-01-10 16:15:39 +01:00
bbmap biology/bbmap: Update to 38.92 2021-08-22 08:59:58 -05:00
bcftools biology/bcftools: Update to 1.14 2021-12-18 11:56:51 -06:00
bedtools
bfc biology/bfc: Correct sequencing errors from Illumina sequencing data 2021-08-23 12:28:41 -05:00
bio-mocha bio-mocha: Build plugin against bcftools 1.14, the current port 2021-12-21 10:17:11 -06:00
bioawk
biococoa
biolibc biology/biolibc: Update to 0.2.1 2021-12-14 13:45:31 -06:00
biolibc-tools biology/biolibc-tools: Update to 0.1.1 2021-12-14 13:45:32 -06:00
bioparser biology/bioparser: Update 3.0.12-2 -> 3.0.15 2021-09-21 09:41:49 -07:00
biosig biology/biosig: Add DISTNAME instead of DISTVERSIONSUFFIX 2021-08-16 19:57:30 -07:00
biosoup
biostar-tools biology/biostar-tools: Allow package build on non-amd64 systems 2021-12-01 09:49:28 -06:00
bolt-lmm
bowtie biology/bowtie: enable on riscv64 2021-12-15 13:55:57 +01:00
bowtie2 biology/bowtie2: Update to 2.4.4 2021-05-24 11:35:43 -05:00
bwa biology/bwa: don't use GCC on powerpc64le 2021-12-01 17:34:18 +00:00
canu biology/canu: fix CATEGORIES 2021-12-20 12:59:13 +00:00
cd-hit biology/cd-hit: fix build on armv7 2021-11-21 13:26:44 +00:00
cdbfasta
checkm math/py-matplotlib: chase minimum Python version in dependent ports 2021-05-10 22:13:20 +02:00
clustal-omega
clustalw
cufflinks Fix CONFLICTS entries of multiple ports 2022-01-10 16:15:39 +01:00
cytoscape biology/cytoscape: mark unconditionally BROKEN 2021-05-12 14:55:52 +03:00
ddocent cleanup: drop support for EOL FreeBSD 11.X 2021-09-30 23:23:30 +02:00
diamond biology/diamond: Update to 2.0.13 2021-11-11 13:17:24 -04:00
dsr-pdb
edlib biology/edlib: Update 1.2.6.20201202 -> 1.2.7 2021-08-21 10:12:15 -07:00
emboss */*: Remove redundant '-[0-9]*' from CONFLICTS 2021-10-29 11:50:18 +02:00
erminej biology/erminej: Analyses of gene sets, e.g. gene expression profiling 2021-07-09 07:26:58 -05:00
exonerate
fasta Fix CONFLICTS entries of multiple ports 2022-01-10 16:15:39 +01:00
fasta3 Deorbit RESTRICTED && NO_CDROM, part one. 2021-05-06 13:47:41 +02:00
fastahack
fastdnaml
fastool
fastp biology/fastp: Update to 0.23.2 2021-12-30 10:30:30 -06:00
fastqc
fasttree biology/fasttree: fix build on armv7 2021-06-15 08:41:19 +00:00
fastx-toolkit
figtree
flash biology/flash: Fast Length Adjustment of SHort reads 2021-08-23 12:26:47 -05:00
fluctuate
freebayes biology/freebayes: enable on riscv64 2021-12-17 14:26:57 +01:00
garlic
gatk
gcta
gemma math/gsl: update to 2.7 2021-06-16 21:31:27 +02:00
generand
gff2ps
gffread Fix CONFLICTS entries of multiple ports 2022-01-10 16:15:39 +01:00
gmap Fix CONFLICTS entries of multiple ports 2022-01-10 16:15:39 +01:00
gperiodic
graphlan
groopm math/py-matplotlib: chase minimum Python version in dependent ports 2021-05-10 22:13:20 +02:00
haplohseq
hhsuite biology/hhsuite: fix packaging on powerpc 2021-11-16 12:03:42 +00:00
hisat2 biology/hisat2: enable on riscv64 2021-12-16 22:38:56 +01:00
hmmer
htslib biology/htslib: Update to 1.14 2021-12-18 11:56:50 -06:00
hyphy biology/hyphy: Update to 2.5.33 2021-11-17 07:51:41 -04:00
igv cleanup: drop support for EOL FreeBSD 11.X 2021-09-30 23:23:30 +02:00
infernal
iolib biology/iolib: Drop maintainership 2021-05-19 20:56:24 +01:00
iqtree
jalview cleanup: drop support for EOL FreeBSD 11.X 2021-09-30 23:23:30 +02:00
jellyfish *: Clean up some things 2021-10-12 17:01:38 +02:00
kallisto
lamarc
libbigwig
libgff biology/libgff: GFF/GTF parsing library based on GCLib 2021-12-05 14:50:42 -06:00
libgtextutils
libneurosim biology/libneurosim: New port: Common interfaces for neuronal simulators 2021-10-08 10:20:27 -07:00
libnuml biology/libnuml: New port: C++ library for Numerical Markup Language 2021-09-18 23:47:02 -07:00
libsbml biology/libsbml: Fix build with Python 3.10 2021-11-02 05:28:40 +08:00
libsedml biology/libsedml: New port: C++ SED-ML library 2021-09-19 11:15:35 -07:00
linux-foldingathome Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.) 2021-10-25 12:58:29 +00:00
mafft biology/mafft: Update to 7.267 2021-10-22 13:11:23 +08:00
mapm3
migrate
minimap2 biology/minimap2: Update to 2.24 2021-12-31 08:30:52 -06:00
mmseqs2 biology/mmseqs2: disable on 32-bits 2021-09-12 21:05:53 +00:00
molden biology/molden: update to 6.7 2022-01-05 17:01:00 -06:00
mopac
mothur biology/mothur: Update 1.46.0 -> 1.46.1 2021-09-02 02:29:56 -07:00
mrbayes *: Remove unnecessary 'port' argument from USES=readline 2021-05-15 09:14:04 +02:00
mummer Fix CONFLICTS entries of multiple ports 2022-01-10 16:15:39 +01:00
muscle
ncbi-blast+ Fix CONFLICTS entries of multiple ports 2022-01-10 16:15:39 +01:00
ncbi-cxx-toolkit Fix CONFLICTS entries of multiple ports 2022-01-10 16:15:39 +01:00
ncbi-entrez-direct Fix CONFLICTS entries of multiple ports 2022-01-10 16:15:39 +01:00
ncbi-toolkit
ncbi-vdb
ngs-sdk biology/ngs-sdk: Update 2.11.0-> 2.11.1 2021-08-18 10:17:44 -07:00
p5-AcePerl
p5-Bio-ASN1-EntrezGene
p5-Bio-Cluster
p5-Bio-Coordinate
p5-Bio-Das
p5-Bio-Das-Lite
p5-Bio-DB-EMBL
p5-Bio-DB-NCBIHelper biology/p5-Bio-DB-NCBIHelper: Update to 1.7.7 2021-07-06 22:56:10 +08:00
p5-Bio-FeatureIO
p5-Bio-GFF3
p5-Bio-Glite
p5-Bio-Graphics
p5-Bio-MAGETAB
p5-Bio-NEXUS
p5-Bio-Phylo
p5-Bio-SCF
p5-Bio-Variation
p5-BioPerl
p5-BioPerl-Run
p5-transdecoder
p5-TrimGalore
paml
pbbam *: fix tab vs. space issues, and comments according to the guide. 2021-10-16 11:51:39 +02:00
pbseqan *: fix tab vs. space issues, and comments according to the guide. 2021-10-16 11:51:39 +02:00
peak-classifier biology/peak-classifier: Update to 0.1.2 2021-12-14 13:45:32 -06:00
pear-merger
phrap Deorbit RESTRICTED && NO_CDROM, part two. 2021-05-06 13:47:48 +02:00
phred Deorbit RESTRICTED && NO_CDROM, part two. 2021-05-06 13:47:48 +02:00
phyml biology/phyml: update to 3.3.20211231 2022-01-02 18:31:24 +01:00
picard-tools
plink
pooler biology/pooler: fix build on powerpc 2021-10-06 20:52:30 +00:00
primer3
prodigal
prodigy-lig
protomol
psi88
py-biom-format
py-biopython biology/py-biopython: Update to 1.79 2021-10-12 14:43:04 +08:00
py-bx-python biology/py-bx-python: Update 0.8.11-6 -> 0.8.13 2021-12-21 01:03:57 -08:00
py-crossmap biology/py-crossmap: chase ad5a0604c4 2021-10-14 00:53:16 +00:00
py-cutadapt biology/py-cutadapt: Update strict py-dnaio dep version 2021-05-04 08:20:39 -05:00
py-deeptools biology/py-deeptools: User-friendly tools for exploring deep-sequencing data 2021-10-14 06:51:12 -05:00
py-deeptoolsintervals biology/py-deeptoolsintervals: Python interface for deepTools interval trees 2021-10-13 11:02:13 -05:00
py-dnaio biology/py-dnaio: Update to 0.5.1 2021-05-04 08:19:25 -05:00
py-ete3
py-Genesis-PyAPI
py-gffutils
py-goatools biology/py-goatools: Tools for processing and visualizing Gene Ontology terms 2021-07-02 12:00:29 -05:00
py-gtfparse
py-hits
py-libnuml biology/py-libnuml: fix install with python 3.10+ 2021-11-02 21:08:32 +03:00
py-libsedml biology/py-libsedml: fix install with python 3.10+ 2021-11-02 21:08:31 +03:00
py-loompy
py-macs2
py-multiqc math/py-matplotlib: chase minimum Python version in dependent ports 2021-05-10 22:13:20 +02:00
py-ont-fast5-api biology/py-ont-fast5-api: Interface to Oxford Nanopore .fast5 files 2021-08-13 08:34:09 -05:00
py-orange3-bioinformatics biology/py-orange3-bioinformatics: Update 3.2.2 -> 4.3.1 2021-04-27 01:56:19 -07:00
py-orange3-single-cell
py-pandas-charm
py-py2bit biology/py-py2bit: Python interface for 2bit packed nucleotide files 2021-10-13 07:53:53 -05:00
py-pybigwig biology/py-bigwig: Rename to biology/py-pybigwig 2021-10-13 16:21:32 -05:00
py-pyfaidx
py-pysam biology/py-pysam: Update 0.16.0.1 -> 0.18.0 2021-12-19 23:48:52 -08:00
py-PySCeS biology/py-PySCeS: Update 0.9.8a -> 1.0.0 2021-09-20 14:34:22 -07:00
py-python-libsbml biology/py-python-libsbml: limit supported python versions, fix build 2021-11-03 21:26:41 +03:00
py-pywgsim biology/py-pywgsim: Modified wgsim genomic data simulator 2021-09-06 07:55:49 -05:00
py-resdk biology/py-resdk: Update 13.7.0 -> 13.8.0 2021-12-29 21:15:52 -08:00
py-scikit-bio
py-xenaPython
pyfasta
python-nexus
rainbow
rampler
readseq
recombine
ruby-bio Fix CONFLICTS entries of multiple ports 2022-01-10 16:15:39 +01:00
rubygem-bio biology/rubygem-bio: Update to 2.0.2 2021-07-01 04:44:06 +08:00
rubygem-bio-executables
rubygem-bio-old-biofetch-emulator
rubygem-bio-shell Fix CONFLICTS entries of multiple ports 2022-01-10 16:15:39 +01:00
sam2pairwise biology/sam2pairwise: Show pairwise alignment for each read in a SAM file 2021-09-07 15:32:29 -05:00
samtools biology/samtools: Update to 1.14 2021-12-18 11:56:51 -06:00
scrm
seaview biology/seaview: Update version 5.0.4=>5.0.5 2021-12-05 19:02:42 -06:00
seqan */*: Remove redundant '-[0-9]*' from CONFLICTS 2021-10-29 11:50:18 +02:00
seqan1
seqan3 biology/seqan3: Update 3.0.3 -> 3.1.0 2021-11-14 21:18:53 -08:00
seqan-apps */*: Remove compiler:openmp from Mk/Uses/compiler.mk 2021-10-03 19:47:27 +02:00
seqio
seqkit biology/seqkit: Update 2.0.1 -> 2.1.0 2021-11-16 10:57:47 -08:00
seqtk biology/seqtk: Update to 1.3 2021-12-18 13:37:06 -06:00
sigviewer misc/: Update 0.99.6-2 -> 0.991 2021-08-18 10:17:45 -07:00
sim4
slclust
smithwaterman
snpeff
spoa
sra-tools Fix CONFLICTS entries of multiple ports 2022-01-10 16:15:39 +01:00
stacks
star biology/star: Update to 2.7.9a 2021-11-26 15:57:02 -06:00
stringtie
subread
tabixpp
taxonkit biology/taxonkit: Update 0.8.0 -> 0.9.0 2021-12-02 12:57:06 -08:00
treekin biology/treekin: Unbreak 2021-10-15 08:50:24 -07:00
treepuzzle
trimadap Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.) 2021-10-25 12:58:29 +00:00
trimmomatic
tRNAscan-SE
ucsc-userapps Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.) 2021-10-25 12:58:29 +00:00
ugene biology/ugene: update UniPro UGENE to version 40.1 (bugfix release). 2021-10-14 11:23:37 +00:00
unikmer biology/unikmer: Update 0.18.4 -> 0.18.8 2021-09-26 01:54:07 -07:00
vcf2hap biology/vcf2hap: Update to 0.1.4 2021-12-14 13:45:32 -06:00
vcf-split biology/vcf-split: Update to 0.1.3.3 2021-12-14 13:45:32 -06:00
vcflib biology/vcflib: unbreak on riscv64 2021-12-16 22:49:25 +01:00
vcftools biology/vcftools: Add CPE information 2021-09-25 20:28:38 +00:00
velvet
viennarna math/gsl: update to 2.7 2021-06-16 21:31:27 +02:00
vsearch biology/vsearch: Update to 2.19.0 2022-01-07 18:04:02 -06:00
vt
wise
Makefile biology/libgff: GFF/GTF parsing library based on GCLib 2021-12-05 14:50:42 -06:00