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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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Installation: nothing provides requested ensembl-vep 102** #3353

Closed rchekaluk closed 3 years ago

rchekaluk commented 3 years ago

Version info

To Reproduce Exact bcbio command you have used:

sudo apt-get  -y update
sudo apt-get  -y install aptitude
sudo DEBIAN_FRONTEND=noninteractive aptitude -y update
sudo DEBIAN_FRONTEND=noninteractive aptitude -y safe-upgrade
wget https://raw.github.com/chapmanb/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py
tooldir="--tooldir=/usr/local"
aligners="--aligners bwa --aligners bowtie2"
sudo python3 bcbio_nextgen_install.py /usr/local/share/bcbio $tooldir $aligners

Observed behavior Error message or bcbio output:

Checking for problematic or migrated packages in default environment
Initalling initial set of packages for default environment with mamba
# Installing into conda environment default: age-metasv, arriba, bamtools=2.4.0, bamutil, bbmap, bcbio-prioritize, bcbio-variation, bcbio-variation-recall, bcftools, bedops, bedtools=2.27.1, bio-vcf, biobambam, bowtie, bowtie2, break-point-inspector, bwa, bwakit, cage, cancerit-allelecount, chipseq-greylist, cnvkit, coincbc, cramtools, cufflinks, cyvcf2, deeptools, delly, duphold, ensembl-vep=102.*, express, extract-sv-reads, fastp, fastqc>=0.11.8=1, fgbio, freebayes=1.1.0.46, gatk, gatk4, geneimpacts, genesplicer, gffcompare, goleft, grabix, gridss, gsort, gvcfgenotyper, h5py, hisat2, hmftools-amber, hmftools-cobalt, hmftools-purple, hmmlearn, hts-nim-tools, htslib, impute2, kallisto>=0.43.1, kraken, ldc>=1.13.0, lofreq, macs2, maxentscan, mbuffer, minimap2, mintmap, mirdeep2=2.0.0.7, mirtop, moreutils, multiqc, multiqc-bcbio, ngs-disambiguate, novoalign, octopus>=0.5.1b, oncofuse, optitype>=1.3.4, parallel, pbgzip, peddy, perl-sanger-cgp-battenberg, picard, pindel, pizzly, pyloh, pysam>=0.14.0, pythonpy, qsignature, qualimap, rapmap, razers3=3.5.0, rtg-tools, sailfish, salmon, sambamba, samblaster, samtools=1.9, scalpel, seq2c<2016, seqbuster, seqcluster, seqtk, sickle-trim, simple_sv_annotation, singlecell-barcodes, snap-aligner=1.0dev.97, snpeff=4.3.1t, solvebio, spades, staden_io_lib, star=2.6.1d, stringtie, subread, survivor, tdrmapper, tophat-recondition, trim-galore, ucsc-bedgraphtobigwig, ucsc-bedtobigbed, ucsc-bigbedinfo, ucsc-bigbedsummary, ucsc-bigbedtobed, ucsc-bigwiginfo, ucsc-bigwigsummary, ucsc-bigwigtobedgraph, ucsc-bigwigtowig, ucsc-fatotwobit, ucsc-gtftogenepred, ucsc-liftover, ucsc-wigtobigwig, umis, vardict, vardict-java, variantbam, varscan, vcfanno, vcflib, verifybamid2, viennarna, vqsr_cnn, vt, wham, anaconda-client, awscli, bzip2, ncurses, nodejs, p7zip, readline, s3gof3r, xz, perl-app-cpanminus, perl-archive-extract, perl-archive-zip, perl-bio-db-sam, perl-cgi, perl-dbi, perl-encode-locale, perl-file-fetch, perl-file-sharedir, perl-file-sharedir-install, perl-ipc-system-simple, perl-lwp-protocol-https, perl-lwp-simple, perl-statistics-descriptive, perl-time-hires, perl-vcftools-vcf, bioconductor-annotate, bioconductor-apeglm, bioconductor-biocgenerics, bioconductor-biocinstaller, bioconductor-biocstyle, bioconductor-biostrings, bioconductor-biovizbase, bioconductor-bsgenome.hsapiens.ucsc.hg19, bioconductor-bsgenome.hsapiens.ucsc.hg38, bioconductor-bubbletree, bioconductor-cn.mops, bioconductor-copynumber, bioconductor-degreport, bioconductor-deseq2, bioconductor-dexseq, bioconductor-dnacopy, bioconductor-genomeinfodbdata, bioconductor-genomicranges, bioconductor-iranges, bioconductor-limma, bioconductor-rtracklayer, bioconductor-snpchip, bioconductor-titancna, bioconductor-vsn>=3.50.0, r-base, r-basejump=0.7.2, r-bcbiornaseq>=0.2.7, r-cghflasso, r-chbutils, r-devtools, r-dplyr, r-dt, r-ggdendro, r-ggplot2, r-ggrepel>=0.7, r-gplots, r-gsalib, r-knitr, r-pheatmap, r-plyr, r-pscbs, r-reshape, r-rmarkdown, r-rsqlite, r-sleuth, r-snow, r-stringi, r-viridis>=0.5, r-wasabi, r=3.5.1, xorg-libxt
Encountered problems while solving.
Problem: nothing provides requested ensembl-vep 102**

Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - ensembl-vep=102

Expected behavior bcbio should be installed

Log files

Additional context

hackdna commented 3 years ago

Looks like it is due to this change: https://github.com/chapmanb/cloudbiolinux/commit/95ca39653cc828df7da91615cab0b123d36c159f

$ conda search ensembl-vep
Loading channels: done
# Name                       Version           Build  Channel
ensembl-vep                     96.3 pl526hecc5488_0  bioconda
ensembl-vep                     97.0 pl526hecc5488_0  bioconda
ensembl-vep                     97.1 pl526hecc5488_0  bioconda
ensembl-vep                     97.2 pl526hecc5488_0  bioconda
ensembl-vep                     97.3 pl526hecc5488_0  bioconda
ensembl-vep                     97.4 pl526hecc5488_0  bioconda
ensembl-vep                     98.0 pl526hecc5488_0  bioconda
ensembl-vep                     98.0 pl526hecc5488_1  bioconda
ensembl-vep                     98.1 pl526hecc5488_0  bioconda
ensembl-vep                     98.2 pl526hecc5488_0  bioconda
ensembl-vep                     98.3 pl526hecc5488_0  bioconda
ensembl-vep                     99.0 pl526hecc5488_0  bioconda
ensembl-vep                     99.1 pl526hecc5488_0  bioconda
ensembl-vep                     99.2 pl526hecc5488_0  bioconda
ensembl-vep                    100.0 pl526hecc5488_0  bioconda
ensembl-vep                    100.1 pl526hecc5488_0  bioconda
ensembl-vep                    100.1 pl526hecda079_1  bioconda
ensembl-vep                    100.2 pl526hecda079_0  bioconda
ensembl-vep                    100.3 pl526hecda079_0  bioconda
ensembl-vep                    100.4 pl526hecda079_0  bioconda
ensembl-vep                    101.0 pl526hecda079_0  bioconda
roryk commented 3 years ago

Thanks, can you revert that change for now? Looks like ensembl-vep 102 isn't released on their repo yet so we're still on 101.