Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

ensembl-vep=103.1 won't install into miniconda3 #29069

Closed
alanhoyle opened this issue Jun 16, 2021 · 5 comments
Closed

ensembl-vep=103.1 won't install into miniconda3 #29069

alanhoyle opened this issue Jun 16, 2021 · 5 comments

Comments

@alanhoyle
Copy link

I'm trying to install ensembl-vep=103.1 into a Docker image. I'd like to be using continuumio/miniconda3 to stay future-proof with Python3, but if I do that, it won't work.

FROM continuumio/miniconda3:latest

RUN     conda update conda && \
    conda config --add channels defaults && \
    conda config --add channels bioconda && \
    conda config --add channels conda-forge

RUN conda install ensembl-vep=103.1

If I run docker build on this I get the following error:

[+] Building 101.4s (6/6) FINISHED
 => [internal] load build definition from Dockerfile                                                     0.0s
 => => transferring dockerfile: 333B                                                                     0.0s
 => [internal] load .dockerignore                                                                        0.0s
 => => transferring context: 2B                                                                          0.0s
 => [internal] load metadata for docker.io/continuumio/miniconda3:latest                                 0.0s
 => CACHED [1/3] FROM docker.io/continuumio/miniconda3:latest                                            0.0s
 => [2/3] RUN     conda update conda &&     conda config --add channels defaults &&     conda config -  11.2s
 => ERROR [3/3] RUN conda install ensembl-vep=103.1                                                     90.1s
------
 > [3/3] RUN conda install ensembl-vep=103.1:
#6 0.591 Collecting package metadata (current_repodata.json): ...working... done
#6 10.73 Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
#6 10.73 Collecting package metadata (repodata.json): ...working... done
#6 45.57 Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.

#6 86.34 Found conflicts! Looking for incompatible packages.
#6 86.34 This can take several minutes.  Press CTRL-C to abort.
#6 86.34 failed
#6 86.34
#6 86.34 UnsatisfiableError: The following specifications were found to be incompatible with each other:
#6 86.34
#6 86.34 Output in format: Requested package -> Available versions
#6 86.34
#6 86.34 Package xz conflicts for:
#6 86.34 python=3.8 -> xz[version='>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0']
#6 86.34 ensembl-vep=103.1 -> htslib -> xz[version='5.2.*|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0']
#6 86.34
#6 86.34 Package libstdcxx-ng conflicts for:
#6 86.34 python=3.8 -> libffi[version='>=3.2.1,<3.3.0a0'] -> libstdcxx-ng[version='>=4.9|>=7.2.0']
#6 86.34 python=3.8 -> libstdcxx-ng[version='>=7.3.0|>=7.5.0|>=9.3.0']
#6 86.34
#6 86.34 Package libgcc-ng conflicts for:
#6 86.34 python=3.8 -> libgcc-ng[version='>=7.3.0|>=7.5.0|>=9.3.0']
#6 86.34 python=3.8 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libgcc-ng[version='>=4.9|>=7.2.0']
#6 86.34
------
executor failed running [/bin/sh -c conda install ensembl-vep=103.1]: exit code: 1

However, if I change to continuumio/miniconda (i.e. the older Python2 version) it works.

+] Building 348.4s (7/7) FINISHED
 => [internal] load build definition from Dockerfile                                                     0.0s
 => => transferring dockerfile: 332B                                                                     0.0s
 => [internal] load .dockerignore                                                                        0.0s
 => => transferring context: 2B                                                                          0.0s
 => [internal] load metadata for docker.io/continuumio/miniconda:latest                                  0.0s
 => CACHED [1/3] FROM docker.io/continuumio/miniconda:latest                                             0.0s
 => [2/3] RUN     conda update conda &&     conda config --add channels defaults &&     conda config -  21.1s
 => [3/3] RUN conda install ensembl-vep=103.1                                                          317.8s
 => exporting to image                                                                                   9.4s
 => => exporting layers                                                                                  9.4s
 => => writing image sha256:9c87217033045[....]

With more complex Dockerfiles, I've seen some other issues related to perl-bioperl>=1.7.2 and t_coffee vs t-coffee needing a Python < 3.8 and >= 3.7 (default is 3.8.5). (see #20459 for more examples of that)
@matthdsm
Copy link
Contributor

Why not use the biocontainers version?
docker pull quay.io/biocontainers/ensembl-vep:103.1--pl5262h4a94de4_2
https://biocontainers.pro/tools/ensembl-vep.

These images are built in essentially the same way as you're trying to to.
M

@alanhoyle
Copy link
Author

This is part of a workflow and our container strategy is to create one image per workflow version. That way we version the whole shebang in parallel and only need to distribute the workflow and the associated image. VEP is only one tool of many in the workflow.

@0xaf1f 0xaf1f mentioned this issue Jan 25, 2022
Closed
@rpetit3
Copy link
Member

rpetit3 commented Feb 1, 2022

Heads up, I was able to create an environment

conda create -n test-ensemble -c conda-forge -c bioconda 'ensembl-vep=103.1'
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.10.3
  latest version: 4.11.0

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /home/robert_petit/miniconda3/envs/test-ensemble

  added / updated specs:
    - ensembl-vep=103.1


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    atk-1.0-2.36.0             |       h3371d22_4         560 KB  conda-forge
    cairo-1.16.0               |    ha00ac49_1009         1.5 MB  conda-forge
    clustalw-2.1               |       h7d875b9_6         318 KB  bioconda
    ensembl-vep-103.1          | pl5262h4a94de4_2         3.0 MB  bioconda
    expat-2.4.4                |       h9c3ff4c_0         183 KB  conda-forge
    font-ttf-dejavu-sans-mono-2.37|       hab24e00_0         388 KB  conda-forge
    font-ttf-inconsolata-3.000 |       h77eed37_0          94 KB  conda-forge
    font-ttf-source-code-pro-2.038|       h77eed37_0         684 KB  conda-forge
    font-ttf-ubuntu-0.83       |       hab24e00_0         1.9 MB  conda-forge
    fontconfig-2.13.94         |       ha180cfb_0         323 KB  conda-forge
    fonts-conda-ecosystem-1    |                0           4 KB  conda-forge
    fonts-conda-forge-1        |                0           4 KB  conda-forge
    freetype-2.10.4            |       h0708190_1         890 KB  conda-forge
    fribidi-1.0.10             |       h36c2ea0_0         112 KB  conda-forge
    gdk-pixbuf-2.42.6          |       h04a7f16_0         609 KB  conda-forge
    gettext-0.19.8.1           |    h73d1719_1008         3.6 MB  conda-forge
    giflib-5.2.1               |       h36c2ea0_2          77 KB  conda-forge
    graphite2-1.3.13           |    h58526e2_1001         102 KB  conda-forge
    graphviz-2.50.0            |       h8e749b2_2         3.0 MB  conda-forge
    gtk2-2.24.33               |       h90689f9_2         7.4 MB  conda-forge
    gts-0.7.6                  |       h64030ff_2         411 KB  conda-forge
    harfbuzz-3.3.1             |       hb4a5f5f_0         2.2 MB  conda-forge
    htslib-1.12                |       h9093b5e_1         2.1 MB  bioconda
    libdb-6.2.32               |       h9c3ff4c_0        23.3 MB  conda-forge
    libedit-3.1.20191231       |       he28a2e2_2         121 KB  conda-forge
    libgd-2.3.3                |       h3cfcdeb_1         267 KB  conda-forge
    libpng-1.6.37              |       h21135ba_2         306 KB  conda-forge
    librsvg-2.52.5             |       h0a9e6e8_2         5.3 MB  conda-forge
    libtool-2.4.6              |    h9c3ff4c_1008         511 KB  conda-forge
    libuuid-2.32.1             |    h7f98852_1000          28 KB  conda-forge
    libwebp-1.2.2              |       h3452ae3_0          85 KB  conda-forge
    libwebp-base-1.2.2         |       h7f98852_1         824 KB  conda-forge
    libxcb-1.13                |    h7f98852_1004         391 KB  conda-forge
    libxslt-1.1.33             |       h0ef7038_3         521 KB  conda-forge
    mysql-connector-c-6.1.11   |    h6eb9d5d_1007         2.7 MB  conda-forge
    paml-4.9                   |       h779adbc_6         1.2 MB  bioconda
    pango-1.50.3               |       h9967ed3_0         458 KB  conda-forge
    perl-aceperl-1.92          |          pl526_2         149 KB  bioconda
    perl-algorithm-diff-1.1903 |          pl526_2          34 KB  bioconda
    perl-algorithm-munkres-0.08|          pl526_1          11 KB  bioconda
    perl-apache-test-1.40      |          pl526_1         115 KB  bioconda
    perl-app-cpanminus-1.7044  |          pl526_1         234 KB  bioconda
    perl-appconfig-1.71        |          pl526_1          42 KB  bioconda
    perl-array-compare-3.0.1   |          pl526_1          12 KB  bioconda
    perl-autoloader-5.74       |          pl526_2           5 KB  bioconda
    perl-base-2.23             |          pl526_1          10 KB  bioconda
    perl-bio-asn1-entrezgene-1.73| pl5262hdfd78af_2          23 KB  bioconda
    perl-bio-coordinate-1.007001| pl5262hdfd78af_2          35 KB  bioconda
    perl-bio-db-hts-3.01       | pl5262h22771d5_3         123 KB  bioconda
    perl-bio-featureio-1.6.905 | pl5262hdfd78af_3          40 KB  bioconda
    perl-bio-phylo-0.58        | pl5262hdfd78af_3         310 KB  bioconda
    perl-bio-samtools-1.43     |  pl526h1341992_1         172 KB  bioconda
    perl-bio-tools-phylo-paml-1.7.3| pl5262hdfd78af_2          57 KB  bioconda
    perl-bio-tools-run-alignment-clustalw-1.7.4| pl5262hdfd78af_2          25 KB  bioconda
    perl-bio-tools-run-alignment-tcoffee-1.7.4| pl5262hdfd78af_3          24 KB  bioconda
    perl-bioperl-1.7.2         |         pl526_11          13 KB  bioconda
    perl-bioperl-core-1.007002 | pl5262hdfd78af_3         3.2 MB  bioconda
    perl-bioperl-run-1.007002  | pl5262hdfd78af_5         431 KB  bioconda
    perl-business-isbn-3.004   |          pl526_0          15 KB  bioconda
    perl-business-isbn-data-20140910.003|          pl526_0          15 KB  bioconda
    perl-cache-cache-1.08      |          pl526_0          31 KB  bioconda
    perl-capture-tiny-0.48     |          pl526_0          17 KB  bioconda
    perl-cgi-4.44              |  pl526h14c3975_1         116 KB  bioconda
    perl-class-data-inheritable-0.08|          pl526_1           7 KB  bioconda
    perl-class-inspector-1.34  |          pl526_0          14 KB  bioconda
    perl-class-load-0.25       |          pl526_0          12 KB  bioconda
    perl-class-load-xs-0.10    |  pl526h6bb024c_2          13 KB  bioconda
    perl-class-method-modifiers-2.12|          pl526_0          13 KB  bioconda
    perl-clone-0.42            |  pl526h516909a_0          13 KB  bioconda
    perl-constant-1.33         |          pl526_1          10 KB  bioconda
    perl-convert-binary-c-0.78 |  pl526h6bb024c_3         252 KB  bioconda
    perl-convert-binhex-1.125  |          pl526_1          25 KB  bioconda
    perl-crypt-rc4-2.02        |          pl526_1           8 KB  bioconda
    perl-data-dumper-2.173     |          pl526_0          35 KB  bioconda
    perl-data-optlist-0.110    |          pl526_2          10 KB  bioconda
    perl-data-stag-0.14        |          pl526_1          78 KB  bioconda
    perl-date-format-2.30      |          pl526_2          29 KB  bioconda
    perl-db-file-1.855         |  pl526h516909a_0          53 KB  bioconda
    perl-dbd-mysql-4.046       |  pl526h6bb024c_1         227 KB  bioconda
    perl-dbd-sqlite-1.64       |  pl526h516909a_0         2.3 MB  bioconda
    perl-dbi-1.642             |          pl526_0         549 KB  bioconda
    perl-devel-globaldestruction-0.14|          pl526_0           7 KB  bioconda
    perl-devel-overloadinfo-0.005|          pl526_0           8 KB  bioconda
    perl-devel-stacktrace-2.04 |          pl526_0          16 KB  bioconda
    perl-digest-hmac-1.03      |          pl526_3           9 KB  bioconda
    perl-digest-md5-2.55       |          pl526_0          18 KB  bioconda
    perl-digest-perl-md5-1.9   |          pl526_1          11 KB  bioconda
    perl-digest-sha1-2.13      |  pl526h6bb024c_1          20 KB  bioconda
    perl-dist-checkconflicts-0.11|          pl526_2          10 KB  bioconda
    perl-dynaloader-1.25       |          pl526_1           3 KB  bioconda
    perl-email-date-format-1.005|          pl526_2           8 KB  bioconda
    perl-encode-2.88           |          pl526_1         2.1 MB  bioconda
    perl-encode-locale-1.05    |          pl526_6          11 KB  bioconda
    perl-error-0.17027         |          pl526_1          20 KB  bioconda
    perl-eval-closure-0.14     |  pl526h6bb024c_4          11 KB  bioconda
    perl-exception-class-1.44  |          pl526_0          19 KB  bioconda
    perl-file-listing-6.04     |          pl526_1           9 KB  bioconda
    perl-file-path-2.16        |          pl526_0          17 KB  bioconda
    perl-file-slurp-tiny-0.004 |          pl526_1           8 KB  bioconda
    perl-file-sort-1.01        |          pl526_2          18 KB  bioconda
    perl-file-temp-0.2304      |          pl526_2          26 KB  bioconda
    perl-file-which-1.23       |          pl526_0          12 KB  bioconda
    perl-font-afm-1.20         |          pl526_2          14 KB  bioconda
    perl-font-ttf-1.06         |          pl526_0         200 KB  bioconda
    perl-gd-2.68               |  pl526he941832_0         112 KB  bioconda
    perl-getopt-long-2.50      |          pl526_1          27 KB  bioconda
    perl-graph-0.9704          |          pl526_1          73 KB  bioconda
    perl-graphviz-2.24         |  pl526h734ff71_0          36 KB  bioconda
    perl-html-element-extended-1.18|          pl526_1          24 KB  bioconda
    perl-html-entities-numbered-0.04|          pl526_1          11 KB  bioconda
    perl-html-formatter-2.16   |          pl526_0          30 KB  bioconda
    perl-html-parser-3.72      |  pl526h6bb024c_5          66 KB  bioconda
    perl-html-tableextract-2.13|          pl526_2          23 KB  bioconda
    perl-html-tagset-3.20      |          pl526_3          12 KB  bioconda
    perl-html-tidy-1.60        |          pl526_0          20 KB  bioconda
    perl-html-tree-5.07        |          pl526_1         129 KB  bioconda
    perl-html-treebuilder-xpath-0.14|          pl526_1          12 KB  bioconda
    perl-http-cookies-6.04     |          pl526_0          19 KB  bioconda
    perl-http-daemon-6.01      |          pl526_1          14 KB  bioconda
    perl-http-date-6.02        |          pl526_3          10 KB  bioconda
    perl-http-message-6.18     |          pl526_0          51 KB  bioconda
    perl-http-negotiate-6.01   |          pl526_3          13 KB  bioconda
    perl-image-info-1.38       |          pl526_1          41 KB  bioconda
    perl-image-size-3.300      |          pl526_2          26 KB  bioconda
    perl-io-html-1.001         |          pl526_2          13 KB  bioconda
    perl-io-sessiondata-1.03   |          pl526_1           8 KB  bioconda
    perl-io-socket-ssl-2.066   |          pl526_0         151 KB  bioconda
    perl-io-string-1.08        |          pl526_3          10 KB  bioconda
    perl-io-stringy-2.111      |          pl526_1          35 KB  bioconda
    perl-io-tty-1.12           |          pl526_1          30 KB  bioconda
    perl-ipc-run-20180523.0    |          pl526_0          74 KB  bioconda
    perl-ipc-sharelite-0.17    |  pl526h6bb024c_1          24 KB  bioconda
    perl-jcode-2.07            |          pl526_2          24 KB  bioconda
    perl-lib-0.63              |          pl526_1           6 KB  bioconda
    perl-libwww-perl-6.39      |          pl526_0          94 KB  bioconda
    perl-libxml-perl-0.08      |          pl526_2          38 KB  bioconda
    perl-lwp-mediatypes-6.04   |          pl526_0          22 KB  bioconda
    perl-lwp-protocol-https-6.07|          pl526_4           9 KB  bioconda
    perl-lwp-simple-6.15       |  pl526h470a237_4         348 KB  bioconda
    perl-mailtools-2.21        |          pl526_0          48 KB  bioconda
    perl-math-cdf-0.1          |  pl526h14c3975_5          69 KB  bioconda
    perl-math-derivative-1.01  |          pl526_0           9 KB  bioconda
    perl-math-random-0.72      |  pl526h14c3975_2          55 KB  bioconda
    perl-math-spline-0.02      |          pl526_2           8 KB  bioconda
    perl-mime-base64-3.15      |          pl526_1          15 KB  bioconda
    perl-mime-lite-3.030       |          pl526_1          51 KB  bioconda
    perl-mime-tools-5.508      |          pl526_1         113 KB  bioconda
    perl-mime-types-2.17       |          pl526_0          56 KB  bioconda
    perl-mldbm-2.05            |          pl526_1          15 KB  bioconda
    perl-module-implementation-0.09|          pl526_2           9 KB  bioconda
    perl-module-runtime-0.016  |          pl526_1          15 KB  bioconda
    perl-module-runtime-conflicts-0.003|          pl526_0           7 KB  bioconda
    perl-moo-2.003004          |          pl526_0          38 KB  bioconda
    perl-moose-2.2011          |  pl526hf484d3e_1         444 KB  bioconda
    perl-mozilla-ca-20180117   |          pl526_1         140 KB  bioconda
    perl-mro-compat-0.13       |          pl526_0          10 KB  bioconda
    perl-net-http-6.19         |          pl526_0          19 KB  bioconda
    perl-net-ssleay-1.88       |  pl526h90d6eec_0         289 KB  bioconda
    perl-ntlm-1.09             |          pl526_4          15 KB  bioconda
    perl-ole-storage_lite-0.19 |          pl526_3          18 KB  bioconda
    perl-package-deprecationmanager-0.17|          pl526_0          10 KB  bioconda
    perl-package-stash-0.38    |  pl526hf484d3e_1          66 KB  bioconda
    perl-package-stash-xs-0.28 |  pl526hf484d3e_1          21 KB  bioconda
    perl-params-util-1.07      |  pl526h6bb024c_4          14 KB  bioconda
    perl-parent-0.236          |          pl526_1           5 KB  bioconda
    perl-parse-recdescent-1.967015|          pl526_0          71 KB  bioconda
    perl-pdf-api2-2.035        |          pl526_0         2.3 MB  bioconda
    perl-perlio-gzip-0.20      |  pl526h84994c4_1          17 KB  bioconda
    perl-pod-escapes-1.07      |          pl526_1          10 KB  bioconda
    perl-pod-usage-1.69        |          pl526_1          13 KB  bioconda
    perl-postscript-0.06       |          pl526_2          22 KB  bioconda
    perl-role-tiny-2.000008    |          pl526_0          15 KB  bioconda
    perl-sereal-4.007          |          pl526_0          10 KB  bioconda
    perl-sereal-decoder-4.007  |  pl526h14c3975_0         139 KB  bioconda
    perl-sereal-encoder-4.007  |  pl526h14c3975_0         174 KB  bioconda
    perl-set-intervaltree-0.12 |  pl526he1b5a44_0          30 KB  bioconda
    perl-set-scalar-1.29       |          pl526_2          19 KB  bioconda
    perl-soap-lite-1.19        |          pl526_1         117 KB  bioconda
    perl-socket-2.027          |          pl526_1          31 KB  bioconda
    perl-sort-naturally-1.03   |          pl526_2          14 KB  bioconda
    perl-spreadsheet-parseexcel-0.65|          pl526_2          63 KB  bioconda
    perl-spreadsheet-writeexcel-2.40|          pl526_2         259 KB  bioconda
    perl-statistics-descriptive-3.0702|          pl526_0          32 KB  bioconda
    perl-storable-3.15         |  pl526h14c3975_0          63 KB  bioconda
    perl-sub-exporter-0.987    |          pl526_2          30 KB  bioconda
    perl-sub-exporter-progressive-0.001013|          pl526_0           8 KB  bioconda
    perl-sub-identify-0.14     |  pl526h14c3975_0          12 KB  bioconda
    perl-sub-install-0.928     |          pl526_2          10 KB  bioconda
    perl-sub-name-0.21         |          pl526_1          13 KB  bioconda
    perl-sub-quote-2.006003    |          pl526_1          18 KB  bioconda
    perl-sub-uplevel-0.2800    |  pl526h14c3975_2          13 KB  bioconda
    perl-svg-2.84              |          pl526_0          37 KB  bioconda
    perl-svg-graph-0.02        |          pl526_3          26 KB  bioconda
    perl-task-weaken-1.06      |          pl526_0           8 KB  bioconda
    perl-template-toolkit-2.26 |          pl526_1         319 KB  bioconda
    perl-test-1.26             |          pl526_1          14 KB  bioconda
    perl-test-deep-1.128       |          pl526_1          36 KB  bioconda
    perl-test-differences-0.67 |          pl526_0          15 KB  bioconda
    perl-test-exception-0.43   |          pl526_2          12 KB  bioconda
    perl-test-harness-3.42     |          pl526_0          82 KB  bioconda
    perl-test-leaktrace-0.16   |  pl526h14c3975_2          23 KB  bioconda
    perl-test-most-0.35        |          pl526_0          18 KB  bioconda
    perl-test-requiresinternet-0.05|          pl526_0           7 KB  bioconda
    perl-test-warn-0.36        |          pl526_1          13 KB  bioconda
    perl-text-csv-2.00         |          pl526_0          66 KB  bioconda
    perl-text-diff-1.45        |          pl526_0          20 KB  bioconda
    perl-tie-ixhash-1.23       |          pl526_2          11 KB  bioconda
    perl-time-hires-1.9760     |  pl526h14c3975_1          25 KB  bioconda
    perl-time-local-1.28       |          pl526_1          10 KB  bioconda
    perl-timedate-2.30         |          pl526_1          29 KB  bioconda
    perl-tree-dag_node-1.31    |          pl526_0          40 KB  bioconda
    perl-try-tiny-0.30         |          pl526_1          17 KB  bioconda
    perl-type-tiny-1.004004    |          pl526_0         119 KB  bioconda
    perl-unicode-map-0.112     |  pl526h6bb024c_3         254 KB  bioconda
    perl-uri-1.76              |          pl526_0          55 KB  bioconda
    perl-www-robotrules-6.02   |          pl526_3          12 KB  bioconda
    perl-xml-dom-1.46          |          pl526_0          56 KB  bioconda
    perl-xml-dom-xpath-0.14    |          pl526_1           9 KB  bioconda
    perl-xml-filter-buffertext-1.01|          pl526_2           7 KB  bioconda
    perl-xml-libxml-2.0132     |  pl526h7ec2d77_1         260 KB  bioconda
    perl-xml-libxslt-1.94      |          pl526_1          40 KB  bioconda
    perl-xml-namespacesupport-1.12|          pl526_0          11 KB  bioconda
    perl-xml-parser-2.44_01    |pl5262hc3e0081_1002         165 KB  conda-forge
    perl-xml-regexp-0.04       |          pl526_2           8 KB  bioconda
    perl-xml-sax-1.02          |          pl526_0          36 KB  bioconda
    perl-xml-sax-base-1.09     |          pl526_0          19 KB  bioconda
    perl-xml-sax-expat-0.51    |          pl526_3          10 KB  bioconda
    perl-xml-sax-writer-0.57   |          pl526_0          16 KB  bioconda
    perl-xml-simple-2.25       |          pl526_1          48 KB  bioconda
    perl-xml-twig-3.52         |          pl526_2         144 KB  bioconda
    perl-xml-writer-0.625      |          pl526_2          18 KB  bioconda
    perl-xml-xpath-1.44        |          pl526_0          42 KB  bioconda
    perl-xml-xpathengine-0.14  |          pl526_2          26 KB  bioconda
    perl-yaml-1.29             |          pl526_0          41 KB  bioconda
    pip-22.0.2                 |     pyhd8ed1ab_0         1.5 MB  conda-forge
    pthread-stubs-0.4          |    h36c2ea0_1001           5 KB  conda-forge
    python-3.7.12              |hb7a2778_100_cpython        57.3 MB  conda-forge
    python_abi-3.7             |          2_cp37m           4 KB  conda-forge
    setuptools-60.6.0          |   py37h89c1867_0         1.0 MB  conda-forge
    t_coffee-11.0.8            |   py37hea885bf_8        33.2 MB  bioconda
    tidyp-1.04                 |       h779adbc_3         300 KB  bioconda
    unzip-6.0                  |       h7f98852_2         143 KB  conda-forge
    xorg-kbproto-1.0.7         |    h7f98852_1002          27 KB  conda-forge
    xorg-libice-1.0.10         |       h7f98852_0          58 KB  conda-forge
    xorg-libxau-1.0.9          |       h7f98852_0          13 KB  conda-forge
    xorg-libxdmcp-1.1.3        |       h7f98852_0          19 KB  conda-forge
    xorg-renderproto-0.11.1    |    h7f98852_1002           9 KB  conda-forge
    xorg-xextproto-7.3.0       |    h7f98852_1002          28 KB  conda-forge
    xorg-xproto-7.0.31         |    h7f98852_1007          73 KB  conda-forge
    ------------------------------------------------------------
                                           Total:       179.0 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
  atk-1.0            conda-forge/linux-64::atk-1.0-2.36.0-h3371d22_4
  bzip2              conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
  c-ares             conda-forge/linux-64::c-ares-1.18.1-h7f98852_0
  ca-certificates    conda-forge/linux-64::ca-certificates-2021.10.8-ha878542_0
  cairo              conda-forge/linux-64::cairo-1.16.0-ha00ac49_1009
  clustalw           bioconda/linux-64::clustalw-2.1-h7d875b9_6
  curl               conda-forge/linux-64::curl-7.81.0-h2574ce0_0
  ensembl-vep        bioconda/noarch::ensembl-vep-103.1-pl5262h4a94de4_2
  expat              conda-forge/linux-64::expat-2.4.4-h9c3ff4c_0
  font-ttf-dejavu-s~ conda-forge/noarch::font-ttf-dejavu-sans-mono-2.37-hab24e00_0
  font-ttf-inconsol~ conda-forge/noarch::font-ttf-inconsolata-3.000-h77eed37_0
  font-ttf-source-c~ conda-forge/noarch::font-ttf-source-code-pro-2.038-h77eed37_0
  font-ttf-ubuntu    conda-forge/noarch::font-ttf-ubuntu-0.83-hab24e00_0
  fontconfig         conda-forge/linux-64::fontconfig-2.13.94-ha180cfb_0
  fonts-conda-ecosy~ conda-forge/noarch::fonts-conda-ecosystem-1-0
  fonts-conda-forge  conda-forge/noarch::fonts-conda-forge-1-0
  freetype           conda-forge/linux-64::freetype-2.10.4-h0708190_1
  fribidi            conda-forge/linux-64::fribidi-1.0.10-h36c2ea0_0
  gdk-pixbuf         conda-forge/linux-64::gdk-pixbuf-2.42.6-h04a7f16_0
  gettext            conda-forge/linux-64::gettext-0.19.8.1-h73d1719_1008
  giflib             conda-forge/linux-64::giflib-5.2.1-h36c2ea0_2
  graphite2          conda-forge/linux-64::graphite2-1.3.13-h58526e2_1001
  graphviz           conda-forge/linux-64::graphviz-2.50.0-h8e749b2_2
  gtk2               conda-forge/linux-64::gtk2-2.24.33-h90689f9_2
  gts                conda-forge/linux-64::gts-0.7.6-h64030ff_2
  harfbuzz           conda-forge/linux-64::harfbuzz-3.3.1-hb4a5f5f_0
  htslib             bioconda/linux-64::htslib-1.12-h9093b5e_1
  icu                conda-forge/linux-64::icu-69.1-h9c3ff4c_0
  jbig               conda-forge/linux-64::jbig-2.1-h7f98852_2003
  jpeg               conda-forge/linux-64::jpeg-9e-h7f98852_0
  krb5               conda-forge/linux-64::krb5-1.19.2-hcc1bbae_3
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.36.1-hea4e1c9_2
  lerc               conda-forge/linux-64::lerc-2.2.1-h9c3ff4c_0
  libcurl            conda-forge/linux-64::libcurl-7.81.0-h2574ce0_0
  libdb              conda-forge/linux-64::libdb-6.2.32-h9c3ff4c_0
  libdeflate         conda-forge/linux-64::libdeflate-1.7-h7f98852_5
  libedit            conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
  libev              conda-forge/linux-64::libev-4.33-h516909a_1
  libffi             conda-forge/linux-64::libffi-3.4.2-h7f98852_5
  libgcc-ng          conda-forge/linux-64::libgcc-ng-11.2.0-h1d223b6_12
  libgd              conda-forge/linux-64::libgd-2.3.3-h3cfcdeb_1
  libglib            conda-forge/linux-64::libglib-2.70.2-h174f98d_1
  libgomp            conda-forge/linux-64::libgomp-11.2.0-h1d223b6_12
  libiconv           conda-forge/linux-64::libiconv-1.16-h516909a_0
  libnghttp2         conda-forge/linux-64::libnghttp2-1.46.0-h812cca2_0
  libnsl             conda-forge/linux-64::libnsl-2.0.0-h7f98852_0
  libpng             conda-forge/linux-64::libpng-1.6.37-h21135ba_2
  librsvg            conda-forge/linux-64::librsvg-2.52.5-h0a9e6e8_2
  libssh2            conda-forge/linux-64::libssh2-1.10.0-ha56f1ee_2
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-11.2.0-he4da1e4_12
  libtiff            conda-forge/linux-64::libtiff-4.3.0-hf544144_1
  libtool            conda-forge/linux-64::libtool-2.4.6-h9c3ff4c_1008
  libuuid            conda-forge/linux-64::libuuid-2.32.1-h7f98852_1000
  libwebp            conda-forge/linux-64::libwebp-1.2.2-h3452ae3_0
  libwebp-base       conda-forge/linux-64::libwebp-base-1.2.2-h7f98852_1
  libxcb             conda-forge/linux-64::libxcb-1.13-h7f98852_1004
  libxml2            conda-forge/linux-64::libxml2-2.9.12-h885dcf4_1
  libxslt            conda-forge/linux-64::libxslt-1.1.33-h0ef7038_3
  libzlib            conda-forge/linux-64::libzlib-1.2.11-h36c2ea0_1013
  lz4-c              conda-forge/linux-64::lz4-c-1.9.3-h9c3ff4c_1
  mysql-connector-c  conda-forge/linux-64::mysql-connector-c-6.1.11-h6eb9d5d_1007
  ncurses            conda-forge/linux-64::ncurses-6.3-h9c3ff4c_0
  openssl            conda-forge/linux-64::openssl-1.1.1l-h7f98852_0
  paml               bioconda/linux-64::paml-4.9-h779adbc_6
  pango              conda-forge/linux-64::pango-1.50.3-h9967ed3_0
  pcre               conda-forge/linux-64::pcre-8.45-h9c3ff4c_0
  perl               conda-forge/linux-64::perl-5.26.2-h36c2ea0_1008
  perl-aceperl       bioconda/linux-64::perl-aceperl-1.92-pl526_2
  perl-algorithm-di~ bioconda/linux-64::perl-algorithm-diff-1.1903-pl526_2
  perl-algorithm-mu~ bioconda/linux-64::perl-algorithm-munkres-0.08-pl526_1
  perl-apache-test   bioconda/linux-64::perl-apache-test-1.40-pl526_1
  perl-app-cpanminus bioconda/linux-64::perl-app-cpanminus-1.7044-pl526_1
  perl-appconfig     bioconda/linux-64::perl-appconfig-1.71-pl526_1
  perl-array-compare bioconda/linux-64::perl-array-compare-3.0.1-pl526_1
  perl-autoloader    bioconda/linux-64::perl-autoloader-5.74-pl526_2
  perl-base          bioconda/linux-64::perl-base-2.23-pl526_1
  perl-bio-asn1-ent~ bioconda/noarch::perl-bio-asn1-entrezgene-1.73-pl5262hdfd78af_2
  perl-bio-coordina~ bioconda/noarch::perl-bio-coordinate-1.007001-pl5262hdfd78af_2
  perl-bio-db-hts    bioconda/linux-64::perl-bio-db-hts-3.01-pl5262h22771d5_3
  perl-bio-featureio bioconda/noarch::perl-bio-featureio-1.6.905-pl5262hdfd78af_3
  perl-bio-phylo     bioconda/noarch::perl-bio-phylo-0.58-pl5262hdfd78af_3
  perl-bio-samtools  bioconda/linux-64::perl-bio-samtools-1.43-pl526h1341992_1
  perl-bio-tools-ph~ bioconda/noarch::perl-bio-tools-phylo-paml-1.7.3-pl5262hdfd78af_2
  perl-bio-tools-ru~ bioconda/noarch::perl-bio-tools-run-alignment-clustalw-1.7.4-pl5262hdfd78af_2
  perl-bio-tools-ru~ bioconda/noarch::perl-bio-tools-run-alignment-tcoffee-1.7.4-pl5262hdfd78af_3
  perl-bioperl       bioconda/noarch::perl-bioperl-1.7.2-pl526_11
  perl-bioperl-core  bioconda/noarch::perl-bioperl-core-1.007002-pl5262hdfd78af_3
  perl-bioperl-run   bioconda/noarch::perl-bioperl-run-1.007002-pl5262hdfd78af_5
  perl-business-isbn bioconda/linux-64::perl-business-isbn-3.004-pl526_0
  perl-business-isb~ bioconda/linux-64::perl-business-isbn-data-20140910.003-pl526_0
  perl-cache-cache   bioconda/linux-64::perl-cache-cache-1.08-pl526_0
  perl-capture-tiny  bioconda/linux-64::perl-capture-tiny-0.48-pl526_0
  perl-carp          bioconda/linux-64::perl-carp-1.38-pl526_3
  perl-cgi           bioconda/linux-64::perl-cgi-4.44-pl526h14c3975_1
  perl-class-data-i~ bioconda/linux-64::perl-class-data-inheritable-0.08-pl526_1
  perl-class-inspec~ bioconda/linux-64::perl-class-inspector-1.34-pl526_0
  perl-class-load    bioconda/linux-64::perl-class-load-0.25-pl526_0
  perl-class-load-xs bioconda/linux-64::perl-class-load-xs-0.10-pl526h6bb024c_2
  perl-class-method~ bioconda/linux-64::perl-class-method-modifiers-2.12-pl526_0
  perl-clone         bioconda/linux-64::perl-clone-0.42-pl526h516909a_0
  perl-common-sense  bioconda/linux-64::perl-common-sense-3.74-pl526_2
  perl-compress-raw~ bioconda/linux-64::perl-compress-raw-bzip2-2.087-pl526he1b5a44_0
  perl-compress-raw~ bioconda/linux-64::perl-compress-raw-zlib-2.087-pl526hc9558a2_0
  perl-constant      bioconda/linux-64::perl-constant-1.33-pl526_1
  perl-convert-bina~ bioconda/linux-64::perl-convert-binary-c-0.78-pl526h6bb024c_3
  perl-convert-binh~ bioconda/linux-64::perl-convert-binhex-1.125-pl526_1
  perl-crypt-rc4     bioconda/linux-64::perl-crypt-rc4-2.02-pl526_1
  perl-data-dumper   bioconda/linux-64::perl-data-dumper-2.173-pl526_0
  perl-data-optlist  bioconda/linux-64::perl-data-optlist-0.110-pl526_2
  perl-data-stag     bioconda/linux-64::perl-data-stag-0.14-pl526_1
  perl-date-format   bioconda/linux-64::perl-date-format-2.30-pl526_2
  perl-db-file       bioconda/linux-64::perl-db-file-1.855-pl526h516909a_0
  perl-dbd-mysql     bioconda/linux-64::perl-dbd-mysql-4.046-pl526h6bb024c_1
  perl-dbd-sqlite    bioconda/linux-64::perl-dbd-sqlite-1.64-pl526h516909a_0
  perl-dbi           bioconda/linux-64::perl-dbi-1.642-pl526_0
  perl-devel-global~ bioconda/linux-64::perl-devel-globaldestruction-0.14-pl526_0
  perl-devel-overlo~ bioconda/linux-64::perl-devel-overloadinfo-0.005-pl526_0
  perl-devel-stackt~ bioconda/noarch::perl-devel-stacktrace-2.04-pl526_0
  perl-digest-hmac   bioconda/linux-64::perl-digest-hmac-1.03-pl526_3
  perl-digest-md5    bioconda/linux-64::perl-digest-md5-2.55-pl526_0
  perl-digest-perl-~ bioconda/linux-64::perl-digest-perl-md5-1.9-pl526_1
  perl-digest-sha1   bioconda/linux-64::perl-digest-sha1-2.13-pl526h6bb024c_1
  perl-dist-checkco~ bioconda/linux-64::perl-dist-checkconflicts-0.11-pl526_2
  perl-dynaloader    bioconda/linux-64::perl-dynaloader-1.25-pl526_1
  perl-email-date-f~ bioconda/linux-64::perl-email-date-format-1.005-pl526_2
  perl-encode        bioconda/linux-64::perl-encode-2.88-pl526_1
  perl-encode-locale bioconda/linux-64::perl-encode-locale-1.05-pl526_6
  perl-error         bioconda/linux-64::perl-error-0.17027-pl526_1
  perl-eval-closure  bioconda/linux-64::perl-eval-closure-0.14-pl526h6bb024c_4
  perl-exception-cl~ bioconda/linux-64::perl-exception-class-1.44-pl526_0
  perl-exporter      bioconda/linux-64::perl-exporter-5.72-pl526_1
  perl-exporter-tiny bioconda/linux-64::perl-exporter-tiny-1.002001-pl526_0
  perl-extutils-mak~ bioconda/linux-64::perl-extutils-makemaker-7.36-pl526_1
  perl-file-listing  bioconda/linux-64::perl-file-listing-6.04-pl526_1
  perl-file-path     bioconda/linux-64::perl-file-path-2.16-pl526_0
  perl-file-slurp-t~ bioconda/linux-64::perl-file-slurp-tiny-0.004-pl526_1
  perl-file-sort     bioconda/linux-64::perl-file-sort-1.01-pl526_2
  perl-file-temp     bioconda/linux-64::perl-file-temp-0.2304-pl526_2
  perl-file-which    bioconda/linux-64::perl-file-which-1.23-pl526_0
  perl-font-afm      bioconda/linux-64::perl-font-afm-1.20-pl526_2
  perl-font-ttf      bioconda/linux-64::perl-font-ttf-1.06-pl526_0
  perl-gd            bioconda/linux-64::perl-gd-2.68-pl526he941832_0
  perl-getopt-long   bioconda/linux-64::perl-getopt-long-2.50-pl526_1
  perl-graph         bioconda/linux-64::perl-graph-0.9704-pl526_1
  perl-graphviz      bioconda/linux-64::perl-graphviz-2.24-pl526h734ff71_0
  perl-html-element~ bioconda/linux-64::perl-html-element-extended-1.18-pl526_1
  perl-html-entitie~ bioconda/linux-64::perl-html-entities-numbered-0.04-pl526_1
  perl-html-formatt~ bioconda/linux-64::perl-html-formatter-2.16-pl526_0
  perl-html-parser   bioconda/linux-64::perl-html-parser-3.72-pl526h6bb024c_5
  perl-html-tableex~ bioconda/linux-64::perl-html-tableextract-2.13-pl526_2
  perl-html-tagset   bioconda/linux-64::perl-html-tagset-3.20-pl526_3
  perl-html-tidy     bioconda/linux-64::perl-html-tidy-1.60-pl526_0
  perl-html-tree     bioconda/linux-64::perl-html-tree-5.07-pl526_1
  perl-html-treebui~ bioconda/linux-64::perl-html-treebuilder-xpath-0.14-pl526_1
  perl-http-cookies  bioconda/linux-64::perl-http-cookies-6.04-pl526_0
  perl-http-daemon   bioconda/linux-64::perl-http-daemon-6.01-pl526_1
  perl-http-date     bioconda/linux-64::perl-http-date-6.02-pl526_3
  perl-http-message  bioconda/linux-64::perl-http-message-6.18-pl526_0
  perl-http-negotia~ bioconda/linux-64::perl-http-negotiate-6.01-pl526_3
  perl-image-info    bioconda/linux-64::perl-image-info-1.38-pl526_1
  perl-image-size    bioconda/linux-64::perl-image-size-3.300-pl526_2
  perl-io-compress   bioconda/linux-64::perl-io-compress-2.087-pl526he1b5a44_0
  perl-io-html       bioconda/linux-64::perl-io-html-1.001-pl526_2
  perl-io-sessionda~ bioconda/linux-64::perl-io-sessiondata-1.03-pl526_1
  perl-io-socket-ssl bioconda/linux-64::perl-io-socket-ssl-2.066-pl526_0
  perl-io-string     bioconda/linux-64::perl-io-string-1.08-pl526_3
  perl-io-stringy    bioconda/linux-64::perl-io-stringy-2.111-pl526_1
  perl-io-tty        bioconda/linux-64::perl-io-tty-1.12-pl526_1
  perl-ipc-run       bioconda/linux-64::perl-ipc-run-20180523.0-pl526_0
  perl-ipc-sharelite bioconda/linux-64::perl-ipc-sharelite-0.17-pl526h6bb024c_1
  perl-jcode         bioconda/linux-64::perl-jcode-2.07-pl526_2
  perl-json          bioconda/linux-64::perl-json-4.02-pl526_0
  perl-json-xs       bioconda/linux-64::perl-json-xs-2.34-pl526h6bb024c_3
  perl-lib           bioconda/linux-64::perl-lib-0.63-pl526_1
  perl-libwww-perl   bioconda/noarch::perl-libwww-perl-6.39-pl526_0
  perl-libxml-perl   bioconda/linux-64::perl-libxml-perl-0.08-pl526_2
  perl-list-moreuti~ bioconda/linux-64::perl-list-moreutils-0.428-pl526_1
  perl-list-moreuti~ bioconda/linux-64::perl-list-moreutils-xs-0.428-pl526_0
  perl-lwp-mediatyp~ bioconda/linux-64::perl-lwp-mediatypes-6.04-pl526_0
  perl-lwp-protocol~ bioconda/linux-64::perl-lwp-protocol-https-6.07-pl526_4
  perl-lwp-simple    bioconda/linux-64::perl-lwp-simple-6.15-pl526h470a237_4
  perl-mailtools     bioconda/noarch::perl-mailtools-2.21-pl526_0
  perl-math-cdf      bioconda/linux-64::perl-math-cdf-0.1-pl526h14c3975_5
  perl-math-derivat~ bioconda/linux-64::perl-math-derivative-1.01-pl526_0
  perl-math-random   bioconda/linux-64::perl-math-random-0.72-pl526h14c3975_2
  perl-math-spline   bioconda/linux-64::perl-math-spline-0.02-pl526_2
  perl-mime-base64   bioconda/linux-64::perl-mime-base64-3.15-pl526_1
  perl-mime-lite     bioconda/linux-64::perl-mime-lite-3.030-pl526_1
  perl-mime-tools    bioconda/linux-64::perl-mime-tools-5.508-pl526_1
  perl-mime-types    bioconda/linux-64::perl-mime-types-2.17-pl526_0
  perl-mldbm         bioconda/linux-64::perl-mldbm-2.05-pl526_1
  perl-module-imple~ bioconda/linux-64::perl-module-implementation-0.09-pl526_2
  perl-module-runti~ bioconda/linux-64::perl-module-runtime-0.016-pl526_1
  perl-module-runti~ bioconda/linux-64::perl-module-runtime-conflicts-0.003-pl526_0
  perl-moo           bioconda/linux-64::perl-moo-2.003004-pl526_0
  perl-moose         bioconda/linux-64::perl-moose-2.2011-pl526hf484d3e_1
  perl-mozilla-ca    bioconda/linux-64::perl-mozilla-ca-20180117-pl526_1
  perl-mro-compat    bioconda/linux-64::perl-mro-compat-0.13-pl526_0
  perl-net-http      bioconda/noarch::perl-net-http-6.19-pl526_0
  perl-net-ssleay    bioconda/linux-64::perl-net-ssleay-1.88-pl526h90d6eec_0
  perl-ntlm          bioconda/linux-64::perl-ntlm-1.09-pl526_4
  perl-ole-storage_~ bioconda/linux-64::perl-ole-storage_lite-0.19-pl526_3
  perl-package-depr~ bioconda/linux-64::perl-package-deprecationmanager-0.17-pl526_0
  perl-package-stash bioconda/linux-64::perl-package-stash-0.38-pl526hf484d3e_1
  perl-package-stas~ bioconda/linux-64::perl-package-stash-xs-0.28-pl526hf484d3e_1
  perl-params-util   bioconda/linux-64::perl-params-util-1.07-pl526h6bb024c_4
  perl-parent        bioconda/linux-64::perl-parent-0.236-pl526_1
  perl-parse-recdes~ bioconda/linux-64::perl-parse-recdescent-1.967015-pl526_0
  perl-pathtools     bioconda/linux-64::perl-pathtools-3.75-pl526h14c3975_1
  perl-pdf-api2      bioconda/noarch::perl-pdf-api2-2.035-pl526_0
  perl-perlio-gzip   bioconda/linux-64::perl-perlio-gzip-0.20-pl526h84994c4_1
  perl-pod-escapes   bioconda/linux-64::perl-pod-escapes-1.07-pl526_1
  perl-pod-usage     bioconda/linux-64::perl-pod-usage-1.69-pl526_1
  perl-postscript    bioconda/linux-64::perl-postscript-0.06-pl526_2
  perl-role-tiny     bioconda/noarch::perl-role-tiny-2.000008-pl526_0
  perl-scalar-list-~ bioconda/linux-64::perl-scalar-list-utils-1.52-pl526h516909a_0
  perl-sereal        bioconda/noarch::perl-sereal-4.007-pl526_0
  perl-sereal-decod~ bioconda/linux-64::perl-sereal-decoder-4.007-pl526h14c3975_0
  perl-sereal-encod~ bioconda/linux-64::perl-sereal-encoder-4.007-pl526h14c3975_0
  perl-set-interval~ bioconda/linux-64::perl-set-intervaltree-0.12-pl526he1b5a44_0
  perl-set-scalar    bioconda/linux-64::perl-set-scalar-1.29-pl526_2
  perl-soap-lite     bioconda/linux-64::perl-soap-lite-1.19-pl526_1
  perl-socket        bioconda/linux-64::perl-socket-2.027-pl526_1
  perl-sort-natural~ bioconda/linux-64::perl-sort-naturally-1.03-pl526_2
  perl-spreadsheet-~ bioconda/linux-64::perl-spreadsheet-parseexcel-0.65-pl526_2
  perl-spreadsheet-~ bioconda/linux-64::perl-spreadsheet-writeexcel-2.40-pl526_2
  perl-statistics-d~ bioconda/linux-64::perl-statistics-descriptive-3.0702-pl526_0
  perl-storable      bioconda/linux-64::perl-storable-3.15-pl526h14c3975_0
  perl-sub-exporter  bioconda/linux-64::perl-sub-exporter-0.987-pl526_2
  perl-sub-exporter~ bioconda/linux-64::perl-sub-exporter-progressive-0.001013-pl526_0
  perl-sub-identify  bioconda/linux-64::perl-sub-identify-0.14-pl526h14c3975_0
  perl-sub-install   bioconda/linux-64::perl-sub-install-0.928-pl526_2
  perl-sub-name      bioconda/linux-64::perl-sub-name-0.21-pl526_1
  perl-sub-quote     bioconda/linux-64::perl-sub-quote-2.006003-pl526_1
  perl-sub-uplevel   bioconda/linux-64::perl-sub-uplevel-0.2800-pl526h14c3975_2
  perl-svg           bioconda/linux-64::perl-svg-2.84-pl526_0
  perl-svg-graph     bioconda/linux-64::perl-svg-graph-0.02-pl526_3
  perl-task-weaken   bioconda/linux-64::perl-task-weaken-1.06-pl526_0
  perl-template-too~ bioconda/linux-64::perl-template-toolkit-2.26-pl526_1
  perl-test          bioconda/linux-64::perl-test-1.26-pl526_1
  perl-test-deep     bioconda/linux-64::perl-test-deep-1.128-pl526_1
  perl-test-differe~ bioconda/noarch::perl-test-differences-0.67-pl526_0
  perl-test-excepti~ bioconda/linux-64::perl-test-exception-0.43-pl526_2
  perl-test-harness  bioconda/linux-64::perl-test-harness-3.42-pl526_0
  perl-test-leaktra~ bioconda/linux-64::perl-test-leaktrace-0.16-pl526h14c3975_2
  perl-test-most     bioconda/linux-64::perl-test-most-0.35-pl526_0
  perl-test-require~ bioconda/linux-64::perl-test-requiresinternet-0.05-pl526_0
  perl-test-warn     bioconda/linux-64::perl-test-warn-0.36-pl526_1
  perl-text-csv      bioconda/noarch::perl-text-csv-2.00-pl526_0
  perl-text-diff     bioconda/linux-64::perl-text-diff-1.45-pl526_0
  perl-tie-ixhash    bioconda/linux-64::perl-tie-ixhash-1.23-pl526_2
  perl-time-hires    bioconda/linux-64::perl-time-hires-1.9760-pl526h14c3975_1
  perl-time-local    bioconda/linux-64::perl-time-local-1.28-pl526_1
  perl-timedate      bioconda/linux-64::perl-timedate-2.30-pl526_1
  perl-tree-dag_node bioconda/linux-64::perl-tree-dag_node-1.31-pl526_0
  perl-try-tiny      bioconda/linux-64::perl-try-tiny-0.30-pl526_1
  perl-type-tiny     bioconda/linux-64::perl-type-tiny-1.004004-pl526_0
  perl-types-serial~ bioconda/linux-64::perl-types-serialiser-1.0-pl526_2
  perl-unicode-map   bioconda/linux-64::perl-unicode-map-0.112-pl526h6bb024c_3
  perl-uri           bioconda/linux-64::perl-uri-1.76-pl526_0
  perl-www-robotrul~ bioconda/linux-64::perl-www-robotrules-6.02-pl526_3
  perl-xml-dom       bioconda/linux-64::perl-xml-dom-1.46-pl526_0
  perl-xml-dom-xpath bioconda/linux-64::perl-xml-dom-xpath-0.14-pl526_1
  perl-xml-filter-b~ bioconda/linux-64::perl-xml-filter-buffertext-1.01-pl526_2
  perl-xml-libxml    bioconda/linux-64::perl-xml-libxml-2.0132-pl526h7ec2d77_1
  perl-xml-libxslt   bioconda/linux-64::perl-xml-libxslt-1.94-pl526_1
  perl-xml-namespac~ bioconda/linux-64::perl-xml-namespacesupport-1.12-pl526_0
  perl-xml-parser    conda-forge/linux-64::perl-xml-parser-2.44_01-pl5262hc3e0081_1002
  perl-xml-regexp    bioconda/linux-64::perl-xml-regexp-0.04-pl526_2
  perl-xml-sax       bioconda/noarch::perl-xml-sax-1.02-pl526_0
  perl-xml-sax-base  bioconda/linux-64::perl-xml-sax-base-1.09-pl526_0
  perl-xml-sax-expat bioconda/linux-64::perl-xml-sax-expat-0.51-pl526_3
  perl-xml-sax-writ~ bioconda/linux-64::perl-xml-sax-writer-0.57-pl526_0
  perl-xml-simple    bioconda/linux-64::perl-xml-simple-2.25-pl526_1
  perl-xml-twig      bioconda/linux-64::perl-xml-twig-3.52-pl526_2
  perl-xml-writer    bioconda/linux-64::perl-xml-writer-0.625-pl526_2
  perl-xml-xpath     bioconda/linux-64::perl-xml-xpath-1.44-pl526_0
  perl-xml-xpatheng~ bioconda/linux-64::perl-xml-xpathengine-0.14-pl526_2
  perl-xsloader      bioconda/linux-64::perl-xsloader-0.24-pl526_0
  perl-yaml          bioconda/noarch::perl-yaml-1.29-pl526_0
  pip                conda-forge/noarch::pip-22.0.2-pyhd8ed1ab_0
  pixman             conda-forge/linux-64::pixman-0.40.0-h36c2ea0_0
  pthread-stubs      conda-forge/linux-64::pthread-stubs-0.4-h36c2ea0_1001
  python             conda-forge/linux-64::python-3.7.12-hb7a2778_100_cpython
  python_abi         conda-forge/linux-64::python_abi-3.7-2_cp37m
  readline           conda-forge/linux-64::readline-8.1-h46c0cb4_0
  setuptools         conda-forge/linux-64::setuptools-60.6.0-py37h89c1867_0
  sqlite             conda-forge/linux-64::sqlite-3.37.0-h9cd32fc_0
  t_coffee           bioconda/linux-64::t_coffee-11.0.8-py37hea885bf_8
  tidyp              bioconda/linux-64::tidyp-1.04-h779adbc_3
  tk                 conda-forge/linux-64::tk-8.6.11-h27826a3_1
  unzip              conda-forge/linux-64::unzip-6.0-h7f98852_2
  wheel              conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
  xorg-kbproto       conda-forge/linux-64::xorg-kbproto-1.0.7-h7f98852_1002
  xorg-libice        conda-forge/linux-64::xorg-libice-1.0.10-h7f98852_0
  xorg-libsm         conda-forge/linux-64::xorg-libsm-1.2.3-hd9c2040_1000
  xorg-libx11        conda-forge/linux-64::xorg-libx11-1.7.2-h7f98852_0
  xorg-libxau        conda-forge/linux-64::xorg-libxau-1.0.9-h7f98852_0
  xorg-libxdmcp      conda-forge/linux-64::xorg-libxdmcp-1.1.3-h7f98852_0
  xorg-libxext       conda-forge/linux-64::xorg-libxext-1.3.4-h7f98852_1
  xorg-libxrender    conda-forge/linux-64::xorg-libxrender-0.9.10-h7f98852_1003
  xorg-renderproto   conda-forge/linux-64::xorg-renderproto-0.11.1-h7f98852_1002
  xorg-xextproto     conda-forge/linux-64::xorg-xextproto-7.3.0-h7f98852_1002
  xorg-xproto        conda-forge/linux-64::xorg-xproto-7.0.31-h7f98852_1007
  xz                 conda-forge/linux-64::xz-5.2.5-h516909a_1
  zlib               conda-forge/linux-64::zlib-1.2.11-h36c2ea0_1013
  zstd               conda-forge/linux-64::zstd-1.5.2-ha95c52a_0


Proceed ([y]/n)?

@0xaf1f
Copy link
Contributor

0xaf1f commented Dec 14, 2022

With more complex Dockerfiles, I've seen some other issues related to perl-bioperl>=1.7.2 and t_coffee vs t-coffee needing a Python < 3.8 and >= 3.7 (default is 3.8.5).

@alanhoyle this part at least should now be resolved. (#32576)

@alanhoyle
Copy link
Author

Thanks for letting me know @0xaf1f.

I tested this with a simplified Dockerfile that uses micromamba instead of conda, and was able to get it to build:

FROM mambaorg/micromamba:latest

RUN micromamba install -n base -c conda-forge -c bioconda -c defaults ensembl-vep=103.1

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
4 participants
@alanhoyle @0xaf1f @rpetit3 @matthdsm