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unlhcc / hcc-conda-recipes

Read-only mirror of the HCC conda recipes repo.
http://www.anaconda.org/hcc
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bcl2fastq2 requires libboost version 1.67.0 #11

Open todddeluca opened 3 years ago

todddeluca commented 3 years ago

The command bcl2fastq did not work after installing the bcl2fastq2 package.

This is the installation output:

(mancr) [tdeluca1@vacc-user1 20210630_181823]$ conda config --env --add channels conda-forge
(mancr) [tdeluca1@vacc-user1 20210630_181823]$ conda config --env --add channels bioconda
(mancr) [tdeluca1@vacc-user1 20210630_181823]$ conda install -c hcc bcl2fastq2
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /users/t/d/tdeluca1/miniconda3/envs/mancr

  added / updated specs:
    - bcl2fastq2

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    bcl2fastq2-2.20.0.422      |       hac72e42_0        21.8 MB  hcc
    icu-58.2                   |    hf484d3e_1000        22.6 MB  conda-forge
    libboost-1.73.0            |      h3ff78a5_11        13.9 MB
    zstd-1.4.9                 |       ha95c52a_0         431 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        58.7 MB

The following NEW packages will be INSTALLED:

  bcl2fastq2         hcc/linux-64::bcl2fastq2-2.20.0.422-hac72e42_0
  bzip2              conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
  icu                conda-forge/linux-64::icu-58.2-hf484d3e_1000
  libboost           pkgs/main/linux-64::libboost-1.73.0-h3ff78a5_11
  lz4-c              conda-forge/linux-64::lz4-c-1.9.3-h9c3ff4c_0
  python_abi         conda-forge/linux-64::python_abi-3.9-2_cp39
  zstd               conda-forge/linux-64::zstd-1.4.9-ha95c52a_0

The following packages will be UPDATED:

  ca-certificates    pkgs/main::ca-certificates-2021.5.25-~ --> conda-forge::ca-certificates-2021.5.30-ha878542_0

The following packages will be SUPERSEDED by a higher-priority channel:

  certifi            pkgs/main::certifi-2021.5.30-py39h06a~ --> conda-forge::certifi-2021.5.30-py39hf3d152e_0
  openssl              pkgs/main::openssl-1.1.1k-h27cfd23_0 --> conda-forge::openssl-1.1.1k-h7f98852_0

Proceed ([y]/n)? 

Downloading and Extracting Packages
icu-58.2             | 22.6 MB   | ################################################################################################################################################################################################################################### | 100% 
libboost-1.73.0      | 13.9 MB   | ################################################################################################################################################################################################################################### | 100% 
zstd-1.4.9           | 431 KB    | ################################################################################################################################################################################################################################### | 100% 
bcl2fastq2-2.20.0.42 | 21.8 MB   | ################################################################################################################################################################################################################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

The bcl2fastq command fails when it does not find libboost version 1.67.0. The output of running bcl2fastq is:

(mancr) [tdeluca1@vacc-user1 20210630_181823]$ bcl2fastq --version
bcl2fastq: error while loading shared libraries: libboost_chrono.so.1.67.0: cannot open shared object file: No such file or directory

Installing libboost version 1.67.0 fixes the issue. Here is the output of installing 1.67.0 and running bcl2fastq:

(mancr) [tdeluca1@vacc-user1 20210630_181823]$ conda install libboost=1.67.0
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /users/t/d/tdeluca1/miniconda3/envs/mancr

  added / updated specs:
    - libboost=1.67.0

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    libboost-1.67.0            |       h46d08c1_4        13.0 MB
    ------------------------------------------------------------
                                           Total:        13.0 MB

The following packages will be DOWNGRADED:

  libboost                               1.73.0-h3ff78a5_11 --> 1.67.0-h46d08c1_4

Proceed ([y]/n)? 

Downloading and Extracting Packages
libboost-1.67.0      | 13.0 MB   | ################################################################################################################################################################################################################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(mancr) [tdeluca1@vacc-user1 20210630_181823]$ bcl2fastq --version
BCL to FASTQ file converter
bcl2fastq v2.20.0.422
Copyright (c) 2007-2017 Illumina, Inc.