packages-conda.yaml

---
# some ideas how to debug solving issues
# not pinning is best - easier to solve, assuming latest possible versions
# sometimes pinning means the latest version, say we update the old one by pinning package>=2.0
# in 3 years that pinning pushes the installation down (it is still calculated as lower boundary)
# don't duplicate packages - if a package is in bcbio bioconda recipe, delete it from here
# mind r-base / python / htslib / java differences - their versions create separate solution spaces
# the goal is to make one big main enviroment and isolate problematic packages
channels:
  - conda-forge
  - bioconda
minimal:
  - anaconda-client
  - awscli
  - bzip2
  - ncurses
  - nodejs
  - p7zip
  - readline
  - s3gof3r
  - xz
# currently not included to reduce total size of Docker images
# - pandoc
bio_nextgen:
  # default: python3.7.10  htslib1.13
  # htslib1.14 is too fresh - solving issues
  - age-metasv
  - atropos
  - bamtools
  - bamutil
  # installs samtools, a lot of xorg, openjdk11.0.9.1 - a candidate for isolation
  - bbmap
  # wants to update htslib if unrestricted
  # installs perl 5.32.1
  - bcftools=1.13
  - bedops
  # installed by bcbio bioconda recipe
  # 2.30.0 + pybedtools
  # - bedtools
  # installs boost, curl, libmaus
  # see issue 3650
  - biobambam=2.0.87
  - bowtie
  - break-point-inspector
  - bwa
  # installs ruby
  - bio-vcf
  - cage
  # downgrades joblib
  - cnvkit
  - coincbc
  - cramtools
  # cyvcf2 is installed from bcbio-nextgen.yaml
  # debugpy=1.4.1 may cause solve issues
  # - debugpy=1.4.0=py37he226ad3_0
  - deeptools
  - express
  - fastp
  # tmp pin adapt the wrapper to the new version
  - fastqc=0.11.9
  - geneimpacts
  # installs libgcc 7.20
  - genesplicer
  - gffcompare
  - goleft
  - grabix
  - gsort
  - gsutil
  - gvcfgenotyper
  - h5py=3.3
  - hdf5=1.10
  - hmmlearn
  - hisat2
  # installed by bcbio bioconda recipe
  # - htslib=1.13 
  - htseq
  - impute2
  # kallisto 0.46 downgrades h5py to 3.3.0, to hdf5 1.10.6, kallisto is not working with 3.4.0/1.12.1
  - kallisto=0.46
  # downgrades perl to 5.26.2
  - kraken
  - ldc
  # installed by bcbio bioconda recipe = 7.79.1 required by pysam and mamba
  # - libcurl
  - macs2
  - maxentscan
  - mbuffer
  - minimap2
  - mintmap
  - mirdeep2
  - mirtop
  - moreutils
  - multiqc
  - multiqc-bcbio
  - ngs-disambiguate
  - novoalign
  - oncofuse
  - pandoc
  - parallel
  - pbgzip
  - peddy
  # installed by bcbio conda recipe
  #- pysam>=0.14.0
  - pizzly
  # TODO: re-enable preseq but it pulls in openblas which causes problems with other blas libraries
  # - preseq
  - pythonpy
  - qsignature
  - rapmap
  # installed by optitype
  # - razers3
  - rtg-tools
  - sailfish
  - salmon
  - samblaster
  - samtools=1.13
  - scalpel
  # old versions numbered as 2015.x new versions - 1.3
  - seq2c<2016
  - seqbuster
  - seqcluster
  - seqtk
  - sickle-trim
  - simple_sv_annotation
  - singlecell-barcodes
  - snap-aligner=1.0dev.97
  - snpeff=5.0
  - solvebio
  # downgrades openmp
  - spades
  # installed
  #- staden_io_lib
  - star=2.6.1d
  - stringtie
  - subread
  - survivor
  - tophat-recondition
  - tdrmapper
  - trim-galore
  - ucsc-bedtobigbed
  - ucsc-bigbedinfo
  - ucsc-bigbedsummary
  - ucsc-bigbedtobed
  - ucsc-bedgraphtobigwig
  - ucsc-bigwiginfo
  - ucsc-bigwigsummary
  - ucsc-bigwigtobedgraph
  - ucsc-bigwigtowig
  - ucsc-fatotwobit
  - ucsc-gtftogenepred
  - ucsc-liftover
  - ucsc-wigtobigwig
  - umis
  - wham
  # old versions numbered as 2015.x new versions - 1.8.2
  # ok with r installed, without r installs r3.2.2
  - vardict<=2015
  - vardict-java
  - variantbam
  - varscan
  - vcfanno
  - viennarna
  # a lot of dependencies including QT - separate env?
  - vqsr_cnn
# corrects bcbio install, lift up to bcbio conda recipe
ipython:
  # noarch
  - ipython-cluster-helper=0.6.4=py_0
  - ipython_genutils=0.2.0=py37_0
  # 5x fails
  - traitlets=4.3.3
  # 7x has different interface
  - ipyparallel=6.3.0
  # <6.0.0 pin in requirements isn't applied
  - ipython=7.29.0
#installs many more perl dependencies
perl:
  - perl-app-cpanminus
  - perl-archive-extract
  - perl-archive-zip
  # perl-bio-db-sam is deprecated
  - perl-bio-samtools
  - perl-cgi
  - perl-dbi
  - perl-encode-locale
  - perl-file-fetch
  - perl-file-sharedir
  - perl-file-sharedir-install
  - perl-ipc-system-simple
  - perl-lwp-simple
  - perl-lwp-protocol-https
  # removed due to the perl upgrade
  # needs to be upgraded from https://github.com/cancerit/cgpBattenberg
  # perl-sanger-cgp-battenberg
  - perl-statistics-descriptive
  - perl-time-hires
  - perl-vcftools-vcf
r:
  # default r=4.1 SI=1.22 VA=1.38 htslib1.13
  # r4.0 pushes htslibto 1.10
  - r=4.1=r41hd8ed1ab_1004
  # yes r is two digit, rbase is three
  # another 4.1.1 rbase pushed down htslib
  - r-base=4.1.1=hb67fd72_0
  - xorg-libxt
  - r-chbutils
  - r-devtools
  - r-dplyr
  - r-dt
  - r-janitor
  - r-knitr
  - r-ggdendro
  - r-ggplot2
  - r-ggrepel
  - r-gplots
  - r-gsalib
  - r-pheatmap
  - r-plyr
  - r-pscbs
  - r-reshape
  - r-rmarkdown
  - r-rsqlite
  - r-sleuth
  - r-snow
  - r-stringi
  - r-viridis
  - r-wasabi
  - bioconductor-annotate
  - bioconductor-apeglm
  - bioconductor-biocgenerics
  - bioconductor-biocinstaller
  - bioconductor-biocstyle
  - bioconductor-biostrings
  # 1.22.0 requires r4.1 which gives more solve issues
  # 1.20.0 = r40_0
  - bioconductor-summarizedexperiment
  - bioconductor-biovizbase
  - bioconductor-bsgenome.hsapiens.ucsc.hg19
  - bioconductor-bsgenome.hsapiens.ucsc.hg38
  - bioconductor-bubbletree
  - bioconductor-cn.mops
  - bioconductor-copynumber
  - bioconductor-dnacopy
  - bioconductor-degreport
  - bioconductor-deseq2
  - bioconductor-dexseq
  - bioconductor-genomeinfodbdata
  - bioconductor-genomicranges
  - bioconductor-iranges
  - bioconductor-limma
  # 2.38.0 breaks wasabi!
  - bioconductor-rhdf5
  - bioconductor-rtracklayer
  # no bioconductor-snpchip in bioconda anymore
  # bioconductor-snpchip needed for the TitanCNA wrapper but not listed as a depedency in the formula
  - bioconductor-titancna
  - bioconductor-vsn
  #- r-optparse=1.7.1=r40hc72bb7e_0
  - r-optparse
  - bioconductor-purecn>=2.0.1
  - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene
  - bioconductor-org.hs.eg.db
  - bioconductor-genomeinfodb
  - bioconductor-genomeinfodbdata
  - bioconductor-rtracklayer
  - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene
  - r-tidyverse
  - bioconductor-tximport
  - r-deconstructsigs
r35:
  # for arriba, old r dependencies htslib1.9,
  # libtiff -> libdeflate nightmare
  - r=3.5.1;env=r35
  - r-base=3.5.1;env=r35
  - arriba=1.2.0;env=r35
rbcbiornaseq:
  - r-bcbiornaseq>=0.5.1;env=rbcbiornaseq
# openjdk 8 - waiting for gatk 4.4.0 release in conda to switch to java17
java:
  - fgbio;env=java
  - gatk;env=java
  # fixes log4j
  - gatk4=4.2.5.0;env=java
  - picard=2.27.5;env=java
  # lots of dependencies
  # try removing gridss and hmftools
  # - gridss;env=java
  # - hmftools-amber;env=java
  # - hmftools-cobalt;env=java
  # - hmftools-purple;env=java
  - qualimap;env=java
  - bcbio-prioritize;env=java
  - bcbio-variation;env=java
  # does not work with java11
  - bcbio-variation-recall;env=java
htslib1.12:
  - htslib=1.12;env=htslib1.12
  - octopus>=0.7.4;env=htslib1.12
htslib1.11:
  - htslib=1.11;env=htslib1.11
  - scramble;env=htslib1.11
htslib1.10:
  - htslib=1.10;env=htslib1.10
  - ataqv;env=htslib1.10
  - mosdepth;env=htslib1.10
  - hts-nim-tools;env=htslib1.10
  - pindel;env=htslib1.10
  - ensembl-vep=104;env=htslib1.10
  - perl-bio-db-hts>=3.01;env=htslib1.10
  - cancerit-allelecount;env=htslib1.10
  - delly;env=htslib1.10
  - freebayes;env=htslib1.10
  - vcflib;env=htslib1.10
  - verifybamid2;env=htslib1.10
  # this isn't working for vt normalize
  #- vt;env=htslib1.10
htslib1.12_py3.9:
  - htslib=1.12;env=htslib1.12_py3.9
  - lofreq;env=htslib1.12_py3.9
  - sambamba;env=htslib1.12_py3.9
  - chipseq-greylist;env=htslib1.12_py3.9
htslib1.9:
  - htslib=1.9;env=htslib1.9
  - duphold;env=htslib1.9
  - extract-sv-reads;env=htslib1.9
# stall packages
python3.6:
  # pushes down mamba, libtiff, but not hts
  - bowtie2;env=python3.6
  # uses specific pysam 
  - crossmap;env=python3.6
  - cufflinks;env=python3.6
  - pyloh;env=python3.6
  # vt is tricky, the only combination that works for vt normalize is
  - samtools=1.7;env=python3.6
  - htslib=1.7;env=python3.6
  - vt=2015.11.10=he941832_3;env=python3.6
  # not working in the base py3.7
  - optitype;env=python3.6
  - razers3;env=python3.6
  - pysam=0.15.4;env=python3.6
  - pandas=0.25.3;env=python3.6
#htslib/samtools 1.10
python2:
  - bismark;env=python2
  - cpat;env=python2
  - cutadapt=1.16;env=python2
  # by default 0.30.11 is installed - causes issues with blob gts fields in vcf2db.py/gemini
  - cyvcf2=0.10.0;env=python2
  - dkfz-bias-filter;env=python2
  - gemini;env=python2
  - gvcf-regions;env=python2
  - hap.py;env=python2
  - htslib=1.10;env=python2
  - lumpy-sv;env=python2
  - manta;env=python2
  - metasv;env=python2
  - mirge;env=python2
  - phylowgs;env=python2
  - platypus-variant;env=python2
  - samtools=1.10;env=python2
  - sentieon;env=python2
  - smcounter2;env=python2
  - smoove;env=python2
  - strelka;env=python2
  - svtools;env=python2
  - svtyper;env=python2
  - theta2;env=python2
  - tophat;env=python2
  - vawk;env=python2
  - vcf2db;env=python2
  - numpy=1.16;env=python2
  # for dkfz filter
  # downgrades metasv0.4.0 and libdeflate1.3
  - pysam=0.15.3;env=python2
samtools0:
  # rbase4.1.1 ncurses5.9. samtools0.1.19
  - ericscript;env=samtools0
# samtools 1.7
bwakit:
  - bwakit;env=bwakit
# python3.6
dv:
  - deepvariant;env=dv