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Add a recipe for nanopack. #52963

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merged 4 commits into from
Dec 27, 2024
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A meta package for several other recipes by the same author

Describe your pull request here


Please read the guidelines for Bioconda recipes before opening a pull request (PR).

General instructions

  • If this PR adds or updates a recipe, use "Add" or "Update" appropriately as the first word in its title.
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This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
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Add a run_exports section like this:

build:
  run_exports:
    - ...

with ... being one of:

Case run_exports statement
semantic versioning {{ pin_subpackage("myrecipe", max_pin="x") }}
semantic versioning (0.x.x) {{ pin_subpackage("myrecipe", max_pin="x.x") }}
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…y the same author

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
recipes/nanopack/meta.yaml Outdated Show resolved Hide resolved
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@martin-g
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@BiocondaBot please fetch artifacts

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Package(s) built are ready for inspection:

Arch Package Zip File / Repodata CI Instructions
noarch nanopack-1.1.1-hdfd78af_0.tar.bz2 noarch.zip GitHub Actions
showYou may also use conda to install after downloading and extracting the zip file. conda install -c ./packages <package name>

Docker image(s) built:

Package Tag CI Install with docker
nanopack 1.1.1--hdfd78af_0 GitHub Actions
showImages are in the linux-64 zip file above.gzip -dc images/nanopack---1.1.1--hdfd78af_0.tar.gz | docker load

@martin-g
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nanopack/packages/noarch took 32s 
❯ ll
.rw-r--r-- martin martin 556 B  Mon Dec 23 11:10:08 2024  current_repodata.json
.rw-r--r-- martin martin 382 B  Mon Dec 23 11:10:08 2024  current_repodata.json.bz2
.rw-r--r-- martin martin 2.5 KB Mon Dec 23 11:10:08 2024  index.html
drwxrwxr-x martin martin 4.0 KB Mon Dec 23 14:19:16 2024  info
.rw-r--r-- martin martin  18 KB Mon Dec 23 11:10:08 2024  nanopack-1.1.1-hdfd78af_0.tar.bz2
.rw-r--r-- martin martin 556 B  Mon Dec 23 11:10:08 2024  repodata.json
.rw-r--r-- martin martin 382 B  Mon Dec 23 11:10:08 2024  repodata.json.bz2
.rw-r--r-- martin martin 556 B  Mon Dec 23 11:10:08 2024  repodata_from_packages.json
.rw-r--r-- martin martin 382 B  Mon Dec 23 11:10:08 2024  repodata_from_packages.json.bz2

nanopack/packages/noarch 
❯ conda install -c ./ nanopack
Channels:
 - file:///tmp/nanopack/packages
 - bioconda
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/martin/miniforge3

  added / updated specs:
    - nanopack


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    aws-c-auth-0.8.0           |      h8c8080f_14         105 KB  conda-forge
    aws-c-cal-0.8.1            |       h0f28dba_2          47 KB  conda-forge
    aws-c-common-0.10.5        |       hb9d3cd8_0         232 KB  conda-forge
    aws-c-compression-0.3.0    |       h9cc6398_4          19 KB  conda-forge
    aws-c-event-stream-0.5.0   |      hf811eff_10          53 KB  conda-forge
    aws-c-http-0.9.2           |       hce7dc5d_3         193 KB  conda-forge
    aws-c-io-0.15.3            |       hfd54f12_3         154 KB  conda-forge
    aws-c-mqtt-0.11.0          |      ha3c2ba9_11         189 KB  conda-forge
    aws-c-s3-0.7.5             |       h55e9418_4         111 KB  conda-forge
    aws-c-sdkutils-0.2.1       |       h9cc6398_3          55 KB  conda-forge
    aws-checksums-0.2.2        |       h9cc6398_3          71 KB  conda-forge
    aws-crt-cpp-0.29.7         |       hed26007_5         346 KB  conda-forge
    aws-sdk-cpp-1.11.458       |       h571fd1c_3         2.9 MB  conda-forge
    azure-core-cpp-1.14.0      |       h5cfcd09_0         337 KB  conda-forge
    azure-identity-cpp-1.10.0  |       h113e628_0         227 KB  conda-forge
    azure-storage-blobs-cpp-12.13.0|       h3cf044e_1         536 KB  conda-forge
    azure-storage-common-cpp-12.8.0|       h736e048_1         146 KB  conda-forge
    azure-storage-files-datalake-cpp-12.12.0|       ha633028_1         281 KB  conda-forge
    biopython-1.84             |  py312h9a8786e_0         3.3 MB  conda-forge
    ca-certificates-2024.12.14 |       hbcca054_0         153 KB  conda-forge
    certifi-2024.12.14         |     pyhd8ed1ab_0         158 KB  conda-forge
    conda-24.11.2              |  py312h7900ff3_0         1.1 MB  conda-forge
    cramino-0.15.0             |       h3dc2dae_1         4.1 MB  bioconda
    deprecated-1.2.15          |     pyhd8ed1ab_1          14 KB  conda-forge
    expat-2.6.4                |       h5888daf_0         135 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       |       h77eed37_3         1.5 MB  conda-forge
    fontconfig-2.15.0          |       h7e30c49_1         259 KB  conda-forge
    fonts-conda-forge-1        |                0           4 KB  conda-forge
    gflags-2.2.2               |    h5888daf_1005         117 KB  conda-forge
    glog-0.7.1                 |       hbabe93e_0         140 KB  conda-forge
    kaleido-core-0.2.1         |       h3644ca4_0        59.2 MB  conda-forge
    libabseil-20240722.0       | cxx17_h5888daf_1         1.2 MB  conda-forge
    libarrow-18.1.0            |   h3b07799_4_cpu         8.4 MB  conda-forge
    libarrow-acero-18.1.0      |   h8bbc2ab_4_cpu         596 KB  conda-forge
    libarrow-dataset-18.1.0    |   h8bbc2ab_4_cpu         572 KB  conda-forge
    libarrow-substrait-18.1.0  |   had74209_4_cpu         508 KB  conda-forge
    libblas-3.9.0              |26_linux64_openblas          16 KB  conda-forge
    libcblas-3.9.0             |26_linux64_openblas          16 KB  conda-forge
    libcrc32c-1.1.2            |       h9c3ff4c_0          20 KB  conda-forge
    libdeflate-1.23            |       h4ddbbb0_0          71 KB  conda-forge
    libevent-2.1.12            |       hf998b51_1         417 KB  conda-forge
    libgoogle-cloud-2.31.0     |       h804f50b_0         1.2 MB  conda-forge
    libgoogle-cloud-storage-2.31.0|       h0121fbd_0         764 KB  conda-forge
    libgrpc-1.67.1             |       hc2c308b_0         7.0 MB  conda-forge
    liblapack-3.9.0            |26_linux64_openblas          16 KB  conda-forge
    libparquet-18.1.0          |   hf4f6db6_4_cpu         1.1 MB  conda-forge
    libprotobuf-5.28.2         |       h5b01275_0         2.8 MB  conda-forge
    libre2-11-2024.07.02       |       hbbce691_1         206 KB  conda-forge
    libthrift-0.21.0           |       h0e7cc3e_0         416 KB  conda-forge
    libutf8proc-2.9.0          |       hb9d3cd8_1          80 KB  conda-forge
    mappy-2.28                 |  py312h4711d71_3         171 KB  bioconda
    mathjax-2.7.7              |       ha770c72_3        21.2 MB  conda-forge
    nanocomp-1.24.2            |     pyhdfd78af_0          24 KB  bioconda
    nanofilt-2.8.0             |             py_0          12 KB  bioconda
    nanoget-1.19.3             |     pyhdfd78af_0          34 KB  bioconda
    nanolyse-1.2.1             |     pyhdfd78af_0          41 KB  bioconda
    nanomath-1.4.0             |     pyhdfd78af_0          29 KB  bioconda
    nanopack-1.1.1             |       hdfd78af_0          18 KB  file:///tmp/nanopack/packages
    nanoplot-1.43.0            |     pyhdfd78af_1          37 KB  bioconda
    nanoqc-0.10.0              |     pyhdfd78af_0          27 KB  bioconda
    nanostat-1.6.0             |     pyhdfd78af_0          12 KB  bioconda
    nspr-4.36                  |       h5888daf_0         225 KB  conda-forge
    nss-3.107                  |       hdf54f9c_0         1.9 MB  conda-forge
    numpy-2.2.1                |  py312h7e784f5_0         8.1 MB  conda-forge
    orc-2.0.3                  |       he039a57_0         1.1 MB  conda-forge
    pandas-2.2.3               |  py312hf9745cd_1        14.7 MB  conda-forge
    plotly-5.24.1              |     pyhd8ed1ab_1         7.7 MB  conda-forge
    psutil-6.1.0               |  py312h66e93f0_0         477 KB  conda-forge
    pyarrow-18.1.0             |  py312h7900ff3_0          25 KB  conda-forge
    pyarrow-core-18.1.0        |py312h01725c0_0_cpu         4.4 MB  conda-forge
    pysam-0.22.1               |  py312hcfdcdd7_2         4.4 MB  bioconda
    python-dateutil-2.9.0.post0|     pyhff2d567_1         217 KB  conda-forge
    python-kaleido-0.2.1       |     pyhd8ed1ab_0          18 KB  conda-forge
    python-tzdata-2024.2       |     pyhd8ed1ab_1         139 KB  conda-forge
    pytz-2024.1                |     pyhd8ed1ab_0         184 KB  conda-forge
    re2-2024.07.02             |       h77b4e00_1          26 KB  conda-forge
    s2n-1.5.9                  |       h0fd0ee4_0         347 KB  conda-forge
    scipy-1.14.1               |  py312h62794b6_2        16.6 MB  conda-forge
    six-1.17.0                 |     pyhd8ed1ab_0          16 KB  conda-forge
    snappy-1.2.1               |       h8bd8927_1          42 KB  conda-forge
    sqlite-3.47.0              |       h9eae976_1         863 KB  conda-forge
    tenacity-9.0.0             |     pyhd8ed1ab_1          24 KB  conda-forge
    wrapt-1.17.0               |  py312h66e93f0_0          62 KB  conda-forge
    ------------------------------------------------------------
                                           Total:       185.9 MB

The following NEW packages will be INSTALLED:

  aws-c-auth         conda-forge/linux-64::aws-c-auth-0.8.0-h8c8080f_14 
  aws-c-cal          conda-forge/linux-64::aws-c-cal-0.8.1-h0f28dba_2 
  aws-c-common       conda-forge/linux-64::aws-c-common-0.10.5-hb9d3cd8_0 
  aws-c-compression  conda-forge/linux-64::aws-c-compression-0.3.0-h9cc6398_4 
  aws-c-event-stream conda-forge/linux-64::aws-c-event-stream-0.5.0-hf811eff_10 
  aws-c-http         conda-forge/linux-64::aws-c-http-0.9.2-hce7dc5d_3 
  aws-c-io           conda-forge/linux-64::aws-c-io-0.15.3-hfd54f12_3 
  aws-c-mqtt         conda-forge/linux-64::aws-c-mqtt-0.11.0-ha3c2ba9_11 
  aws-c-s3           conda-forge/linux-64::aws-c-s3-0.7.5-h55e9418_4 
  aws-c-sdkutils     conda-forge/linux-64::aws-c-sdkutils-0.2.1-h9cc6398_3 
  aws-checksums      conda-forge/linux-64::aws-checksums-0.2.2-h9cc6398_3 
  aws-crt-cpp        conda-forge/linux-64::aws-crt-cpp-0.29.7-hed26007_5 
  aws-sdk-cpp        conda-forge/linux-64::aws-sdk-cpp-1.11.458-h571fd1c_3 
  azure-core-cpp     conda-forge/linux-64::azure-core-cpp-1.14.0-h5cfcd09_0 
  azure-identity-cpp conda-forge/linux-64::azure-identity-cpp-1.10.0-h113e628_0 
  azure-storage-blo~ conda-forge/linux-64::azure-storage-blobs-cpp-12.13.0-h3cf044e_1 
  azure-storage-com~ conda-forge/linux-64::azure-storage-common-cpp-12.8.0-h736e048_1 
  azure-storage-fil~ conda-forge/linux-64::azure-storage-files-datalake-cpp-12.12.0-ha633028_1 
  biopython          conda-forge/linux-64::biopython-1.84-py312h9a8786e_0 
  cramino            bioconda/linux-64::cramino-0.15.0-h3dc2dae_1 
  deprecated         conda-forge/noarch::deprecated-1.2.15-pyhd8ed1ab_1 
  expat              conda-forge/linux-64::expat-2.6.4-h5888daf_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-h77eed37_3 
  fontconfig         conda-forge/linux-64::fontconfig-2.15.0-h7e30c49_1 
  fonts-conda-forge  conda-forge/noarch::fonts-conda-forge-1-0 
  freetype           conda-forge/linux-64::freetype-2.12.1-h267a509_2 
  gflags             conda-forge/linux-64::gflags-2.2.2-h5888daf_1005 
  glog               conda-forge/linux-64::glog-0.7.1-hbabe93e_0 
  kaleido-core       conda-forge/linux-64::kaleido-core-0.2.1-h3644ca4_0 
  libabseil          conda-forge/linux-64::libabseil-20240722.0-cxx17_h5888daf_1 
  libarrow           conda-forge/linux-64::libarrow-18.1.0-h3b07799_4_cpu 
  libarrow-acero     conda-forge/linux-64::libarrow-acero-18.1.0-h8bbc2ab_4_cpu 
  libarrow-dataset   conda-forge/linux-64::libarrow-dataset-18.1.0-h8bbc2ab_4_cpu 
  libarrow-substrait conda-forge/linux-64::libarrow-substrait-18.1.0-had74209_4_cpu 
  libblas            conda-forge/linux-64::libblas-3.9.0-26_linux64_openblas 
  libbrotlicommon    conda-forge/linux-64::libbrotlicommon-1.1.0-hb9d3cd8_2 
  libbrotlidec       conda-forge/linux-64::libbrotlidec-1.1.0-hb9d3cd8_2 
  libbrotlienc       conda-forge/linux-64::libbrotlienc-1.1.0-hb9d3cd8_2 
  libcblas           conda-forge/linux-64::libcblas-3.9.0-26_linux64_openblas 
  libcrc32c          conda-forge/linux-64::libcrc32c-1.1.2-h9c3ff4c_0 
  libdeflate         conda-forge/linux-64::libdeflate-1.23-h4ddbbb0_0 
  libevent           conda-forge/linux-64::libevent-2.1.12-hf998b51_1 
  libgfortran        conda-forge/linux-64::libgfortran-14.2.0-h69a702a_1 
  libgfortran5       conda-forge/linux-64::libgfortran5-14.2.0-hd5240d6_1 
  libgoogle-cloud    conda-forge/linux-64::libgoogle-cloud-2.31.0-h804f50b_0 
  libgoogle-cloud-s~ conda-forge/linux-64::libgoogle-cloud-storage-2.31.0-h0121fbd_0 
  libgrpc            conda-forge/linux-64::libgrpc-1.67.1-hc2c308b_0 
  liblapack          conda-forge/linux-64::liblapack-3.9.0-26_linux64_openblas 
  libopenblas        conda-forge/linux-64::libopenblas-0.3.28-pthreads_h94d23a6_1 
  libparquet         conda-forge/linux-64::libparquet-18.1.0-hf4f6db6_4_cpu 
  libpng             conda-forge/linux-64::libpng-1.6.44-hadc24fc_0 
  libprotobuf        conda-forge/linux-64::libprotobuf-5.28.2-h5b01275_0 
  libre2-11          conda-forge/linux-64::libre2-11-2024.07.02-hbbce691_1 
  libthrift          conda-forge/linux-64::libthrift-0.21.0-h0e7cc3e_0 
  libutf8proc        conda-forge/linux-64::libutf8proc-2.9.0-hb9d3cd8_1 
  mappy              bioconda/linux-64::mappy-2.28-py312h4711d71_3 
  mathjax            conda-forge/linux-64::mathjax-2.7.7-ha770c72_3 
  nanocomp           bioconda/noarch::nanocomp-1.24.2-pyhdfd78af_0 
  nanofilt           bioconda/noarch::nanofilt-2.8.0-py_0 
  nanoget            bioconda/noarch::nanoget-1.19.3-pyhdfd78af_0 
  nanolyse           bioconda/noarch::nanolyse-1.2.1-pyhdfd78af_0 
  nanomath           bioconda/noarch::nanomath-1.4.0-pyhdfd78af_0 
  nanopack           packages/noarch::nanopack-1.1.1-hdfd78af_0 
  nanoplot           bioconda/noarch::nanoplot-1.43.0-pyhdfd78af_1 
  nanoqc             bioconda/noarch::nanoqc-0.10.0-pyhdfd78af_0 
  nanostat           bioconda/noarch::nanostat-1.6.0-pyhdfd78af_0 
  nspr               conda-forge/linux-64::nspr-4.36-h5888daf_0 
  nss                conda-forge/linux-64::nss-3.107-hdf54f9c_0 
  numpy              conda-forge/linux-64::numpy-2.2.1-py312h7e784f5_0 
  orc                conda-forge/linux-64::orc-2.0.3-he039a57_0 
  pandas             conda-forge/linux-64::pandas-2.2.3-py312hf9745cd_1 
  plotly             conda-forge/noarch::plotly-5.24.1-pyhd8ed1ab_1 
  psutil             conda-forge/linux-64::psutil-6.1.0-py312h66e93f0_0 
  pyarrow            conda-forge/linux-64::pyarrow-18.1.0-py312h7900ff3_0 
  pyarrow-core       conda-forge/linux-64::pyarrow-core-18.1.0-py312h01725c0_0_cpu 
  pysam              bioconda/linux-64::pysam-0.22.1-py312hcfdcdd7_2 
  python-dateutil    conda-forge/noarch::python-dateutil-2.9.0.post0-pyhff2d567_1 
  python-kaleido     conda-forge/noarch::python-kaleido-0.2.1-pyhd8ed1ab_0 
  python-tzdata      conda-forge/noarch::python-tzdata-2024.2-pyhd8ed1ab_1 
  pytz               conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0 
  re2                conda-forge/linux-64::re2-2024.07.02-h77b4e00_1 
  s2n                conda-forge/linux-64::s2n-1.5.9-h0fd0ee4_0 
  scipy              conda-forge/linux-64::scipy-1.14.1-py312h62794b6_2 
  six                conda-forge/noarch::six-1.17.0-pyhd8ed1ab_0 
  snappy             conda-forge/linux-64::snappy-1.2.1-h8bd8927_1 
  sqlite             conda-forge/linux-64::sqlite-3.47.0-h9eae976_1 
  tenacity           conda-forge/noarch::tenacity-9.0.0-pyhd8ed1ab_1 
  wrapt              conda-forge/linux-64::wrapt-1.17.0-py312h66e93f0_0 

The following packages will be UPDATED:

  ca-certificates                      2024.8.30-hbcca054_0 --> 2024.12.14-hbcca054_0 
  certifi                            2024.8.30-pyhd8ed1ab_0 --> 2024.12.14-pyhd8ed1ab_0 
  conda                             24.11.0-py312h7900ff3_0 --> 24.11.2-py312h7900ff3_0 


Proceed ([y]/n)? y


Downloading and Extracting Packages:
                                                                                                                                                                                                                     
Preparing transaction: done                                                                                                                                                                                          
Verifying transaction: done                                                                                                                                                                                          
Executing transaction: done                                                                                                                                                                                          

LGTM!

@martin-g
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@BiocondaBot please add label

@BiocondaBot BiocondaBot added the please review & merge set to ask for merge label Dec 23, 2024
@bgruening
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What is the advantage of this package in contrast to a environment.yaml file? Why do we need to clone the github repo, if its just a meta-package?

@martin-g
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What is the advantage of this package in contrast to a environment.yaml file?

By using a recipe it is created/maintained at one place. Using a env file will have to be created by each user and maintained by them.

There are several other recipes like this:

./dipcall/meta.yaml
./atlas-gene-annotation-manipulation/meta.yaml
./lepwrap/meta.yaml
./haplogrep/meta.yaml
./pstrain/meta.yaml
./atlas-fastq-provider/meta.yaml

Why do we need to clone the github repo, if its just a meta-package?

Hm, I haven't tried without source: but I'd expect that it will fail. I use git_rev because there is no release/tag in that repo.

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@bgruening bgruening left a comment

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Ok :)

@martin-g martin-g merged commit 09b95d1 into bioconda:master Dec 27, 2024
5 checks passed
@martin-g martin-g deleted the aarch64-nanopack branch December 27, 2024 07:31
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