installing from scratch using ether conda or mamba fails on perl version?

[LeoWelter]

problem, installing from scratch on our HPC fails while trying to install a perl packages:

Encountered problems while solving:
  - package perl-encode-locale-1.05-pl526_6 requires perl >=5.26.2,<5.26.3.0a0, but none of the providers can be installed

I have perl 5.26.3 as default on the system or 5.30.2 or 5.34.1 loadable as module.
thanks for any advice in advance

Version info

• bcbio version (bcbio_nextgen.py --version): 1.2.9
• OS name and version (lsb_release -ds):Red Hat Enterprise Linux 8.4

To Reproduce
Exact bcbio command you have used:

/usr/local/bin/python3
 ../bcbio_nextgen_install.py \
	-u stable \
	--datatarget variation \
	--datatarget rnaseq \
	--cores 32 \
	--tooldir ${TOOLDIR} \
	--isolate \
	--distribution "centos" \
	--mamba \
	--genomes ${GENOMES} \
	${DATADIR}

Your yaml configuration file:

Log files (could be found in work/log)
Please attach (10MB max): bcbio-nextgen-commands.log, and bcbio-nextgen-debug.log.

Checking required dependencies
Installing isolated base python installation
Installing mamba
Collecting package metadata (current_repodata.json): done
Solving environment: done

# All requested packages already installed.

Retrieving notices: ...working... done
Installing conda-build

                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

        mamba (0.24.0) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████


Looking for: ['conda-build', 'mamba=0.24.0']

r/noarch                                                      No change
r/linux-64                                                    No change
pkgs/r/linux-64                                               No change
pkgs/r/noarch                                                 No change
ursky/linux-64                                                No change
ursky/noarch                                                  No change
pkgs/main/noarch                                   817.9kB @ 901.1kB/s  0.3s
bioconda/linux-64                                    4.5MB @   4.1MB/s  1.2s
pkgs/main/linux-64                                   5.0MB @   3.9MB/s  1.3s
conda-forge/noarch                                  10.3MB @   4.4MB/s  2.5s
bioconda/noarch                                      4.1MB @   1.6MB/s  1.7s
conda-forge/linux-64                                27.8MB @   4.0MB/s  7.3s

Pinned packages:
  - python 3.7.*


Transaction

  Prefix: /projects/0/lwc2020006/software/bcbio/1.2.9/data/anaconda

  All requested packages already installed

Installing bcbio-nextgen
--2022-11-21 14:05:48--  https://raw.githubusercontent.com/bcbio/bcbio-nextgen/master/requirements-conda.txt
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.110.133, 185.199.111.133, 185.199.109.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.110.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 20 [text/plain]
Saving to: ‘requirements-conda.txt’

requirements-conda.txt       100%[============================================>]      20  --.-KB/s    in 0s

2022-11-21 14:05:48 (2.23 MB/s) - ‘requirements-conda.txt’ saved [20/20]


                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

        mamba (0.24.0) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████


Looking for: ['bcbio-nextgen']

r/linux-64                                                  Using cache
r/noarch                                                    Using cache
conda-forge/linux-64                                        Using cache
conda-forge/noarch                                          Using cache
bioconda/linux-64                                           Using cache
bioconda/noarch                                             Using cache
pkgs/main/linux-64                                          Using cache
pkgs/main/noarch                                            Using cache
pkgs/r/linux-64                                             Using cache
pkgs/r/noarch                                               Using cache
ursky/noarch                                                  No change
ursky/linux-64                                                No change

Pinned packages:
  - python 3.7.*


Transaction

  Prefix: /projects/0/lwc2020006/software/bcbio/1.2.9/data/anaconda

  All requested packages already installed

Collecting package metadata (current_repodata.json): done
Solving environment: done

# All requested packages already installed.

Retrieving notices: ...working... done
Installing data and third party dependencies
Upgrading bcbio
--2022-11-21 14:06:42--  https://raw.githubusercontent.com/bcbio/bcbio-nextgen/master/requirements-conda.txt
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.109.133, 185.199.108.133, 185.199.111.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.109.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 20 [text/plain]
Saving to: ‘bcbio-update-requirements.txt’

bcbio-update-requirements.tx 100%[============================================>]      20  --.-KB/s    in 0s

2022-11-21 14:06:43 (424 KB/s) - ‘bcbio-update-requirements.txt’ saved [20/20]

Upgrade of bcbio-nextgen code complete.
Upgrading third party tools to latest versions
--2022-11-21 14:06:50--  https://github.com/chapmanb/cloudbiolinux/archive/master.tar.gz
Resolving github.com (github.com)... 140.82.121.4
Connecting to github.com (github.com)|140.82.121.4|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://codeload.github.com/chapmanb/cloudbiolinux/tar.gz/refs/heads/master [following]
--2022-11-21 14:06:51--  https://codeload.github.com/chapmanb/cloudbiolinux/tar.gz/refs/heads/master
Resolving codeload.github.com (codeload.github.com)... 140.82.121.9
Connecting to codeload.github.com (codeload.github.com)|140.82.121.9|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [application/x-gzip]
Saving to: ‘STDOUT’

     0K ........ ........ ........ ........ ........ ........ 6.55M
  3072K ........ ........ ........ .......                    32.6M=0.5s

2022-11-21 14:06:51 (9.56 MB/s) - written to stdout [5195149]

Reading packages from /gpfs/work2/0/lwc2020006/software/bcbio/1.2.9/tmpbcbio-install/cloudbiolinux/contrib/flavor/ngs_pipeline_minimal/packages-conda.yaml
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, atropos, bamtools, bamutil, bbmap, bcftools=1.13, bedops, bio-vcf, biobambam=2.0.87, bowtie, break-point-inspector, bwa, cage, cnvkit, coincbc, cramtools, deeptools, express, fastp, fastqc, geneimpacts, genesplicer, gffcompare, goleft, grabix, gsort, gsutil, gvcfgenotyper, h5py=3.3, hdf5=1.10, hisat2, hmmlearn, htseq, impute2, kallisto=0.46, kraken, ldc, macs2, maxentscan, mbuffer, minimap2, mintmap, mirdeep2, mirtop, moreutils, multiqc, multiqc-bcbio, ngs-disambiguate, novoalign, oncofuse, pandoc, parallel, pbgzip, peddy, pizzly, pythonpy, qsignature, rapmap, rtg-tools, sailfish, salmon, samblaster, samtools=1.13, scalpel, seq2c<2016, seqbuster, seqcluster, seqtk, sickle-trim, simple_sv_annotation, singlecell-barcodes, snap-aligner=1.0dev.97, snpeff=5.0, solvebio, spades, 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-java, vardict<=2015, variantbam, varscan, vcfanno, viennarna, vqsr_cnn, wham, ipyparallel=6.3.0, ipython-cluster-helper=0.6.4=py_0, ipython=7.29.0, ipython_genutils=0.2.0=py37_0, traitlets=4.3.3, 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-sanger-cgp-battenberg, 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-genomeinfodb, bioconductor-genomeinfodbdata, bioconductor-genomeinfodbdata, bioconductor-genomicranges, bioconductor-iranges, bioconductor-limma, bioconductor-org.hs.eg.db, bioconductor-purecn>=2.0.1, bioconductor-rhdf5, bioconductor-rtracklayer, bioconductor-rtracklayer, bioconductor-summarizedexperiment, bioconductor-titancna, bioconductor-txdb.hsapiens.ucsc.hg19.knowngene, bioconductor-txdb.hsapiens.ucsc.hg38.knowngene, bioconductor-tximport, bioconductor-vsn, r-base=4.1.1=hb67fd72_0, r-chbutils, r-deconstructsigs, r-devtools, r-dplyr, r-dt, r-ggdendro, r-ggplot2, r-ggrepel, r-gplots, r-gsalib, r-janitor, r-knitr, r-optparse, r-pheatmap, r-plyr, r-pscbs, r-reshape, r-rmarkdown, r-rsqlite, r-sleuth, r-snow, r-stringi, r-tidyverse, r-viridis, r-wasabi, r=4.1=r41hd8ed1ab_1004, xorg-libxt
Encountered problems while solving:
  - package perl-encode-locale-1.05-pl526_6 requires perl >=5.26.2,<5.26.3.0a0, but none of the providers can be installed

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... cdfailed with initial frozen solve. Retrying with flexible solve.
Solving environment: ...working... ^[[A^[[A^[[A






Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.

Your yaml configuration file:

**Log files (could be found in work/log)**
Please attach (10MB max):  `bcbio-nextgen-commands.log`, and `bcbio-nextgen-debug.log`.

[dnbuckley]

I have also encountered this problem.

[amizeranschi]

Same issue for me: #3686

@naumenko-sa any clue what's going on?

It would be great to bring back support for creating Docker images, given all these recurrent Conda issues for new installs.

[naumenko-sa]

Hi @amizeranschi !
Sorry for the delay: I am refactoring the whole installation script to address the install issues.
SN

[gabeng]

I was very fond of the strategy from bcbio_docker: using a focused, compact tool.yaml config file that installs only a small subset of the full swiss-army knife collection. This avoids the typical dependency hell of conda, given that many tools in the standard installation seem to be unused or outdated.
https://github.com/bcbio/bcbio_docker/blob/19369dde53fe40e624b1086d19570b3024929567/Dockerfile.tools#L13

Will you be going in that direction, @naumenko-sa?

[naumenko-sa]

Hi @gabeng !
I am not sure about the whole CWL direction, however definitely I am going for small images for the typical analyses: variant calling and bulkRNA-seq. First of all I am just inspecting the installation process, removing unnecessary steps, unused packages, making sure PATH/PYTHONPATH is not an issue (the most frequent obstacle).
SN

[naumenko-sa]

Hi @LeoWelter, @dnbuckley, @amizeranschi !

It looks like the perl related issue was due to
https://github.com/chapmanb/cloudbiolinux/blob/master/contrib/flavor/ngs_pipeline_minimal/packages-conda.yaml#L181

My install command:
.bcbio_devel_profie:

BCBIO_HOME=/path-tobcbio_install_test2
PATH=${BCBIO_HOME}/anaconda/bin:${BCBIO_HOME}/tools/bin
PATH=${PATH}:/home/user.aspera/connect/bin:/usr/local/bin:/usr/bin:/opt/puppetlabs/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/opt/dell/srvadmin/bin
export PATH
export CONDA_EXE=
export CONDA_PYTHON_EXE=
export CONDA_PREFIX=
export PYTHONPATH=
# don't add ~/.local to PYTHONPATH
export PYTHONNOUSERSITE=True

. .bcbio
$ which python3
/usr/bin/python3
$ python3 bcbio_nextgen_install.py /path-to/bcbio_install_test2 --tooldir=/path-to/bcbio_install_test2/tools --mamba --nodata

(please note --nodata installation, install data separately)

Please give it a try!

It passes the perl issue for me and installs all environments down to python3.6:

# Installing into conda environment python3.6: bowtie2, crossmap, cufflinks, htslib=1.7, optitype, pandas=0.25.3, pyloh, pysam=0.15.4, razers3, samtools=1.7, vt=2015.11.10=he941832_3
Encountered problems while solving:
  - package libsqlite-3.40.0-h753d276_0 requires libzlib >=1.2.13,<1.3.0a0, but none of the providers can be installed

In my case, mamba solved that conflict and the installation finished successfully.

I'd also call the community to be more active in solving such bugs: the perl one wasn't too complicated.
The way to debug them:

• create a python3.7.10 conda env (python3.7.10 is a default python in base) (or just use one from the interrupted installation)
• try to install packages which are reported in a conflict
• in this case, you'd find that one conda/perl package is deprecated and pushes perl version down, while other packages require newer perl, hence the conflict. the deprecated perl package is replaced with a new one, so we need to update our conda specification
• test and describe the solution, make a PR.

In this case, I also removed battenberg, since we are also using the frozen version of it from some time ago, and it pushes perl down. The battenberg (for subclones and CNV in cancer data) is a little subproject - one would need to have proper data to test the new battenberg, incorporate it into bcbio, update installation script.

SN