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mycobactopia-org / MTBseq-nf

MTBSeq made simple and easy using Nextflow and nf-core standard.
https://doi.org/10.5281/zenodo.5498063
MIT License
8 stars 1 forks source link

Evaluate upgrading the project to use mtbseq-1.0.4 #59

Closed abhi18av closed 2 years ago

abhi18av commented 2 years ago

The conda setup for mtbseq-1.0.3 always runs across the problem mentioned in the MTBseq Github repo (issue-29)

gatk-register not found

abhi18av commented 2 years ago

Na, still runs across the same problem 🤷

abhi18av commented 2 years ago

Continuation of the saga https://github.com/mtb-bioinformatics/mtbseq-nf/issues/54

abhi18av commented 2 years ago

Interestingly - if we use the gatk=3.8.0 from the default noarch subchannel of bioconda then the gatk-register isn't installed.

But if we install via the linux-64 subchannel then it is installed 🤯 

$ mamba create -n bioconda-gatk380 bioconda/linux-64::gatk=3.8.0 🟢 

$ mamba create -n bioconda-gatk380-noarch bioconda::gatk=3.8.0 🔴
abhi18av commented 2 years ago

Hmm, now the transition to mtbseq-1.0.4 might actually be possible!

abhi18av commented 2 years ago

Closing this issue since we've run across problems w.r.t Perl and GATK(3) , please refer https://github.com/mtb-bioinformatics/mtbseq-nf/pull/58#issuecomment-1098923500 for context.

abhi18av commented 1 year ago

The problem still persists upon trying to install the latest version from bioconda

Followed the instructions from https://github.com/ngs-fzb/MTBseq_source#conda

  1. Create the env and download the bioconda package 

    mamba create -n mtbseq-env -c bioconda mtbseq

  2. Download the GATK jar

$ wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2
  1. Try to copy the GATK jar using the gatk-register tool, since gatk3-register doesn't exist.
$ gatk-register GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2
ENV_PREFIX /mnt/lustre/users/econceicao/miniconda3/envs/mtbseq-env
Processing GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 as *.tar.bz2
Extracting GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2
mkdir: cannot create directory '/tmp/gatk': File exists
tar: Ignoring unknown extended header keyword `LIBARCHIVE.creationtime'
tar: Ignoring unknown extended header keyword `SCHILY.dev'
tar: Ignoring unknown extended header keyword `SCHILY.ino'
tar: Ignoring unknown extended header keyword `SCHILY.nlink'
GenomeAnalysisTK-3.8-0-ge9d806836/
tar: Ignoring unknown extended header keyword `LIBARCHIVE.creationtime'
tar: Ignoring unknown extended header keyword `SCHILY.dev'
tar: Ignoring unknown extended header keyword `SCHILY.ino'
tar: Ignoring unknown extended header keyword `SCHILY.nlink'
GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar
Error: Unable to access jarfile ./GenomeAnalysisTK.jar
The version of the jar specified, , does not match the version expected by conda: 3.8

==============

  1. NOTE: This works only after unzipping the tar.bz2 
$ tar -xf GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 --wildcards '*.jar'

tar: Ignoring unknown extended header keyword `LIBARCHIVE.creationtime'
tar: Ignoring unknown extended header keyword `SCHILY.dev'
tar: Ignoring unknown extended header keyword `SCHILY.ino'
tar: Ignoring unknown extended header keyword `SCHILY.nlink'
tar: Ignoring unknown extended header keyword `LIBARCHIVE.creationtime'
tar: Ignoring unknown extended header keyword `SCHILY.dev'
tar: Ignoring unknown extended header keyword `SCHILY.ino'
tar: Ignoring unknown extended header keyword `SCHILY.nlink'
  1. Now we are able to register the JAR 
$ gatk-register GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar
ENV_PREFIX /mnt/lustre/users/econceicao/miniconda3/envs/mtbseq-env
Processing GenomeAnalysisTK.jar as *.jar
jar file specified matches expected version
Copying GenomeAnalysisTK.jar to /mnt/lustre/users/econceicao/miniconda3/envs/mtbseq-env/opt/gatk-3.8
abhi18av commented 1 year ago

Interestingly, the version being installed via the default command is still MTBseq 1.0.3 🤔 

$ MTBseq  --version
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
    LANGUAGE = (unset),
    LC_ALL = (unset),
    LC_CTYPE = "UTF-8",
    LANG = "en_US.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to a fallback locale ("en_US.UTF-8").
MTBseq 1.0.3

However, the bigger problem is the expectation of gatk3 name rather than gatk 

$ MTBseq --check (mtbseq-env)
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
    LANGUAGE = (unset),
    LC_ALL = (unset),
    LC_CTYPE = "UTF-8",
    LANG = "en_US.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to a fallback locale ("en_US.UTF-8").
<INFO>  [2023-02-06 16:23:19]   Found perl module: MCE
<INFO>  [2023-02-06 16:23:19]   Found perl module: Statistics::Basic
<INFO>  [2023-02-06 16:23:19]   Found bwa in your PATH!
<INFO>  [2023-02-06 16:23:19]   Found samtools in your PATH!
<ERROR> [2023-02-06 16:23:19]   gatk3 is not installed or not in your PATH!
abhi18av commented 1 year ago

Even after explicitly installing v-1.0.4, it still says version 1.0.3 😓 

  + mtbseq                           1.0.4  hdfd78af_2           bioconda/noarch          Cached

The version mentioned by the mamba create / install command 

mamba create -n mtbseq-104-env -c bioconda mtbseq=1.0.4

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

        mamba (1.1.0) supported by @QuantStack

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

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

Looking for: ['mtbseq=1.0.4']

bioconda/linux-64                                           Using cache
bioconda/noarch                                             Using cache
conda-forge/linux-64                                        Using cache
pkgs/main/noarch                                              No change
pkgs/r/linux-64                                               No change
pkgs/main/linux-64                                            No change
pkgs/r/noarch                                                 No change
conda-forge/noarch                                  3.7s
Transaction

  Prefix: /mnt/lustre/users/econceicao/miniconda3/envs/mtbseq-104-env

  Updating specs:

   - mtbseq=1.0.4

  Package                          Version  Build                Channel                    Size
──────────────────────────────────────────────────────────────────────────────────────────────────
  Install:
──────────────────────────────────────────────────────────────────────────────────────────────────

  + _libgcc_mutex                      0.1  conda_forge          conda-forge/linux-64     Cached
  + _openmp_mutex                      4.5  2_gnu                conda-forge/linux-64     Cached
  + _r-mutex                         1.0.1  anacondar_1          conda-forge/noarch       Cached
  + binutils_impl_linux-64            2.39  he00db2b_1           conda-forge/linux-64     Cached
  + binutils_linux-64                 2.39  h5fc0e48_11          conda-forge/linux-64     Cached
  + bwa                             0.7.17  h7132678_9           bioconda/linux-64        Cached
  + bwidget                         1.9.14  ha770c72_1           conda-forge/linux-64     Cached
  + bzip2                            1.0.8  h7f98852_4           conda-forge/linux-64     Cached
  + c-ares                          1.11.0  h470a237_1           bioconda/linux-64        Cached
  + ca-certificates              2022.12.7  ha878542_0           conda-forge/linux-64     Cached
  + cairo                           1.16.0  h6cf1ce9_1008        conda-forge/linux-64     Cached
  + curl                            7.71.1  he644dc0_8           conda-forge/linux-64     Cached
  + expat                            2.5.0  h27087fc_0           conda-forge/linux-64     Cached
  + fontconfig                      2.14.2  h14ed4e7_0           conda-forge/linux-64     Cached
  + freetype                        2.12.1  hca18f0e_1           conda-forge/linux-64     Cached
  + fribidi                         1.0.10  h36c2ea0_0           conda-forge/linux-64     Cached
  + gatk                               3.8  py36_0               bioconda/linux-64        Cached
  + gcc_impl_linux-64                9.5.0  h99780fb_19          conda-forge/linux-64     Cached
  + gcc_linux-64                     9.5.0  h4258300_11          conda-forge/linux-64     Cached
  + gettext                         0.21.1  h27087fc_0           conda-forge/linux-64     Cached
  + gfortran_impl_linux-64           9.5.0  hf1096a2_19          conda-forge/linux-64     Cached
  + gfortran_linux-64                9.5.0  hdb51d14_11          conda-forge/linux-64     Cached
  + graphite2                       1.3.13  h58526e2_1001        conda-forge/linux-64     Cached
  + gsl                                2.6  he838d99_2           conda-forge/linux-64     Cached
  + gxx_impl_linux-64                9.5.0  h99780fb_19          conda-forge/linux-64     Cached
  + gxx_linux-64                     9.5.0  h43f449f_11          conda-forge/linux-64     Cached
  + harfbuzz                         2.9.1  h83ec7ef_1           conda-forge/linux-64     Cached
  + icu                               68.2  h9c3ff4c_0           conda-forge/linux-64     Cached
  + jpeg                                9e  h166bdaf_2           conda-forge/linux-64     Cached
  + kernel-headers_linux-64         2.6.32  he073ed8_15          conda-forge/noarch       Cached
  + krb5                            1.17.2  h926e7f8_0           conda-forge/linux-64     Cached
  + ld_impl_linux-64                  2.39  hcc3a1bd_1           conda-forge/linux-64     Cached
  + libblas                          3.9.0  16_linux64_openblas  conda-forge/linux-64     Cached
  + libcblas                         3.9.0  16_linux64_openblas  conda-forge/linux-64     Cached
  + libcurl                         7.71.1  hcdd3856_8           conda-forge/linux-64     Cached
  + libedit                   3.1.20191231  he28a2e2_2           conda-forge/linux-64     Cached
  + libev                             4.33  h516909a_1           conda-forge/linux-64     Cached
  + libffi                           3.4.2  h7f98852_5           conda-forge/linux-64     Cached
  + libgcc-devel_linux-64            9.5.0  h0a57e50_19          conda-forge/linux-64     Cached
  + libgcc-ng                       12.2.0  h65d4601_19          conda-forge/linux-64     Cached
  + libgfortran-ng                  12.2.0  h69a702a_19          conda-forge/linux-64     Cached
  + libgfortran5                    12.2.0  h337968e_19          conda-forge/linux-64     Cached
  + libglib                         2.72.1  h2d90d5f_0           conda-forge/linux-64     Cached
  + libgomp                         12.2.0  h65d4601_19          conda-forge/linux-64     Cached
  + libiconv                          1.17  h166bdaf_0           conda-forge/linux-64     Cached
  + liblapack                        3.9.0  16_linux64_openblas  conda-forge/linux-64     Cached
  + libnghttp2                      1.41.0  hab1572f_1           conda-forge/linux-64     Cached
  + libnsl                           2.0.0  h7f98852_0           conda-forge/linux-64     Cached
  + libopenblas                     0.3.21  pthreads_h78a6416_3  conda-forge/linux-64     Cached
  + libpng                          1.6.39  h753d276_0           conda-forge/linux-64     Cached
  + libsanitizer                     9.5.0  h2f262e1_19          conda-forge/linux-64     Cached
  + libsqlite                       3.40.0  h753d276_0           conda-forge/linux-64     Cached
  + libssh2                         1.10.0  haa6b8db_3           conda-forge/linux-64     Cached
  + libstdcxx-devel_linux-64         9.5.0  h0a57e50_19          conda-forge/linux-64     Cached
  + libstdcxx-ng                    12.2.0  h46fd767_19          conda-forge/linux-64     Cached
  + libtiff                          4.2.0  hf544144_3           conda-forge/linux-64     Cached
  + libuuid                         2.32.1  h7f98852_1000        conda-forge/linux-64     Cached
  + libwebp-base                     1.2.4  h166bdaf_0           conda-forge/linux-64     Cached
  + libxcb                            1.13  h7f98852_1004        conda-forge/linux-64     Cached
  + libxml2                         2.9.12  h72842e0_0           conda-forge/linux-64     Cached
  + libzlib                         1.2.13  h166bdaf_4           conda-forge/linux-64     Cached
  + make                               4.3  hd18ef5c_1           conda-forge/linux-64     Cached
  + mtbseq                           1.0.4  hdfd78af_2           bioconda/noarch          Cached
  + ncurses                            6.3  h27087fc_1           conda-forge/linux-64     Cached
  + openjdk                        8.0.332  h166bdaf_0           conda-forge/linux-64     Cached
  + openssl                         1.1.1s  h0b41bf4_1           conda-forge/linux-64     Cached
  + pango                           1.42.4  h69149e4_5           conda-forge/linux-64     Cached
  + pcre                              8.45  h9c3ff4c_0           conda-forge/linux-64     Cached
  + pcre2                            10.36  h032f7d1_1           conda-forge/linux-64     Cached
  + perl                            5.26.2  h36c2ea0_1008        conda-forge/linux-64     Cached
  + perl-base                         2.23  pl526_1              bioconda/linux-64        Cached
  + perl-carp                         1.38  pl526_3              bioconda/linux-64        Cached
  + perl-constant                     1.33  pl526_1              bioconda/linux-64        Cached
  + perl-exporter                     5.72  pl526_1              bioconda/linux-64        Cached
  + perl-extutils-makemaker           7.36  pl526_1              bioconda/linux-64        Cached
  + perl-file-path                    2.16  pl526_0              bioconda/linux-64        Cached
  + perl-getopt-long                  2.50  pl526_1              bioconda/linux-64        Cached
  + perl-mce                         1.837  pl526_0              bioconda/linux-64        Cached
  + perl-number-format                1.75  pl526_3              bioconda/linux-64        Cached
  + perl-scalar-list-utils            1.52  pl526h516909a_0      bioconda/linux-64        Cached
  + perl-socket                      2.027  pl526_1              bioconda/linux-64        Cached
  + perl-statistics-basic           1.6611  pl526_2              bioconda/linux-64        Cached
  + perl-storable                     3.15  pl526h14c3975_0      bioconda/linux-64        Cached
  + perl-time-hires                 1.9760  pl526h14c3975_1      bioconda/linux-64        Cached
  + perl-xsloader                     0.24  pl526_0              bioconda/linux-64        Cached
  + picard                          2.27.5  hdfd78af_0           bioconda/noarch          Cached
  + pip                             21.3.1  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + pixman                          0.40.0  h36c2ea0_0           conda-forge/linux-64     Cached
  + pthread-stubs                      0.4  h36c2ea0_1001        conda-forge/linux-64     Cached
  + python                          3.6.15  hb7a2778_0_cpython   conda-forge/linux-64     Cached
  + python_abi                         3.6  2_cp36m              conda-forge/linux-64     Cached
  + r-base                           4.0.3  hd23ff56_6           conda-forge/linux-64     Cached
  + readline                         8.1.2  h0f457ee_0           conda-forge/linux-64     Cached
  + samtools                           1.6  h9dace67_6           bioconda/linux-64        Cached
  + sed                                4.8  he412f7d_0           conda-forge/linux-64     Cached
  + setuptools                      58.0.4  py36h5fab9bb_2       conda-forge/linux-64     Cached
  + sqlite                          3.40.0  h4ff8645_0           conda-forge/linux-64     Cached
  + sysroot_linux-64                  2.12  he073ed8_15          conda-forge/noarch       Cached
  + tk                              8.6.12  h27826a3_0           conda-forge/linux-64     Cached
  + tktable                           2.10  hb7b940f_3           conda-forge/linux-64     Cached
  + wheel                           0.37.1  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + xorg-kbproto                     1.0.7  h7f98852_1002        conda-forge/linux-64     Cached
  + xorg-libice                     1.0.10  h7f98852_0           conda-forge/linux-64     Cached
  + xorg-libsm                       1.2.3  hd9c2040_1000        conda-forge/linux-64     Cached
  + xorg-libx11                      1.7.2  h7f98852_0           conda-forge/linux-64     Cached
  + xorg-libxau                      1.0.9  h7f98852_0           conda-forge/linux-64     Cached
  + xorg-libxdmcp                    1.1.3  h7f98852_0           conda-forge/linux-64     Cached
  + xorg-libxext                     1.3.4  h7f98852_1           conda-forge/linux-64     Cached
  + xorg-libxrender                 0.9.10  h7f98852_1003        conda-forge/linux-64     Cached
  + xorg-libxt                       1.2.1  h7f98852_2           conda-forge/linux-64     Cached
  + xorg-renderproto                0.11.1  h7f98852_1002        conda-forge/linux-64     Cached
  + xorg-xextproto                   7.3.0  h7f98852_1002        conda-forge/linux-64     Cached
  + xorg-xproto                     7.0.31  h7f98852_1007        conda-forge/linux-64     Cached
  + xz                               5.2.6  h166bdaf_0           conda-forge/linux-64     Cached
  + zlib                            1.2.13  h166bdaf_4           conda-forge/linux-64     Cached
  + zstd                             1.5.2  h3eb15da_6           conda-forge/linux-64     Cached

  Summary:

  Install: 116 packages

  Total download: 0 B

──────────────────────────────────────────────────────────────────────────────────────────────────

Confirm changes: [Y/n] y

Downloading and Extracting Packages

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

To activate this environment, use

     $ mamba activate mtbseq-104-env

To deactivate an active environment, use

     $ mamba deactivate
abhi18av commented 1 year ago 
$ mamba create -n mtbseq-103-env -c bioconda mtbseq=1.0.3                        (mtbseq-104-env)

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

        mamba (1.1.0) supported by @QuantStack

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

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

Looking for: ['mtbseq=1.0.3']

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

  Prefix: /mnt/lustre/users/econceicao/miniconda3/envs/mtbseq-103-env

  Updating specs:

   - mtbseq=1.0.3

  Package                          Version  Build                Channel                    Size
──────────────────────────────────────────────────────────────────────────────────────────────────
  Install:
──────────────────────────────────────────────────────────────────────────────────────────────────

  + _libgcc_mutex                      0.1  conda_forge          conda-forge/linux-64     Cached
  + _openmp_mutex                      4.5  2_gnu                conda-forge/linux-64     Cached
  + _r-mutex                         1.0.1  anacondar_1          conda-forge/noarch       Cached
  + binutils_impl_linux-64            2.39  he00db2b_1           conda-forge/linux-64     Cached
  + binutils_linux-64                 2.39  h5fc0e48_11          conda-forge/linux-64     Cached
  + bwa                             0.7.17  h7132678_9           bioconda/linux-64        Cached
  + bwidget                         1.9.14  ha770c72_1           conda-forge/linux-64     Cached
  + bzip2                            1.0.8  h7f98852_4           conda-forge/linux-64     Cached
  + c-ares                          1.11.0  h470a237_1           bioconda/linux-64        Cached
  + ca-certificates              2022.12.7  ha878542_0           conda-forge/linux-64     Cached
  + cairo                           1.16.0  h6cf1ce9_1008        conda-forge/linux-64     Cached
  + curl                            7.71.1  he644dc0_8           conda-forge/linux-64     Cached
  + expat                            2.5.0  h27087fc_0           conda-forge/linux-64     Cached
  + fontconfig                      2.14.2  h14ed4e7_0           conda-forge/linux-64     Cached
  + freetype                        2.12.1  hca18f0e_1           conda-forge/linux-64     Cached
  + fribidi                         1.0.10  h36c2ea0_0           conda-forge/linux-64     Cached
  + gatk                               3.8  py36_0               bioconda/linux-64        Cached
  + gcc_impl_linux-64                9.5.0  h99780fb_19          conda-forge/linux-64     Cached
  + gcc_linux-64                     9.5.0  h4258300_11          conda-forge/linux-64     Cached
  + gettext                         0.21.1  h27087fc_0           conda-forge/linux-64     Cached
  + gfortran_impl_linux-64           9.5.0  hf1096a2_19          conda-forge/linux-64     Cached
  + gfortran_linux-64                9.5.0  hdb51d14_11          conda-forge/linux-64     Cached
  + graphite2                       1.3.13  h58526e2_1001        conda-forge/linux-64     Cached
  + gsl                                2.6  he838d99_2           conda-forge/linux-64     Cached
  + gxx_impl_linux-64                9.5.0  h99780fb_19          conda-forge/linux-64     Cached
  + gxx_linux-64                     9.5.0  h43f449f_11          conda-forge/linux-64     Cached
  + harfbuzz                         2.9.1  h83ec7ef_1           conda-forge/linux-64     Cached
  + icu                               68.2  h9c3ff4c_0           conda-forge/linux-64     Cached
  + jpeg                                9e  h166bdaf_2           conda-forge/linux-64     Cached
  + kernel-headers_linux-64         2.6.32  he073ed8_15          conda-forge/noarch       Cached
  + krb5                            1.17.2  h926e7f8_0           conda-forge/linux-64     Cached
  + ld_impl_linux-64                  2.39  hcc3a1bd_1           conda-forge/linux-64     Cached
  + libblas                          3.9.0  16_linux64_openblas  conda-forge/linux-64     Cached
  + libcblas                         3.9.0  16_linux64_openblas  conda-forge/linux-64     Cached
  + libcurl                         7.71.1  hcdd3856_8           conda-forge/linux-64     Cached
  + libedit                   3.1.20191231  he28a2e2_2           conda-forge/linux-64     Cached
  + libev                             4.33  h516909a_1           conda-forge/linux-64     Cached
  + libffi                           3.4.2  h7f98852_5           conda-forge/linux-64     Cached
  + libgcc-devel_linux-64            9.5.0  h0a57e50_19          conda-forge/linux-64     Cached
  + libgcc-ng                       12.2.0  h65d4601_19          conda-forge/linux-64     Cached
  + libgfortran-ng                  12.2.0  h69a702a_19          conda-forge/linux-64     Cached
  + libgfortran5                    12.2.0  h337968e_19          conda-forge/linux-64     Cached
  + libglib                         2.72.1  h2d90d5f_0           conda-forge/linux-64     Cached
  + libgomp                         12.2.0  h65d4601_19          conda-forge/linux-64     Cached
  + libiconv                          1.17  h166bdaf_0           conda-forge/linux-64     Cached
  + liblapack                        3.9.0  16_linux64_openblas  conda-forge/linux-64     Cached
  + libnghttp2                      1.41.0  hab1572f_1           conda-forge/linux-64     Cached
  + libnsl                           2.0.0  h7f98852_0           conda-forge/linux-64     Cached
  + libopenblas                     0.3.21  pthreads_h78a6416_3  conda-forge/linux-64     Cached
  + libpng                          1.6.39  h753d276_0           conda-forge/linux-64     Cached
  + libsanitizer                     9.5.0  h2f262e1_19          conda-forge/linux-64     Cached
  + libsqlite                       3.40.0  h753d276_0           conda-forge/linux-64     Cached
  + libssh2                         1.10.0  haa6b8db_3           conda-forge/linux-64     Cached
  + libstdcxx-devel_linux-64         9.5.0  h0a57e50_19          conda-forge/linux-64     Cached
  + libstdcxx-ng                    12.2.0  h46fd767_19          conda-forge/linux-64     Cached
  + libtiff                          4.2.0  hf544144_3           conda-forge/linux-64     Cached
  + libuuid                         2.32.1  h7f98852_1000        conda-forge/linux-64     Cached
  + libwebp-base                     1.2.4  h166bdaf_0           conda-forge/linux-64     Cached
  + libxcb                            1.13  h7f98852_1004        conda-forge/linux-64     Cached
  + libxml2                         2.9.12  h72842e0_0           conda-forge/linux-64     Cached
  + libzlib                         1.2.13  h166bdaf_4           conda-forge/linux-64     Cached
  + make                               4.3  hd18ef5c_1           conda-forge/linux-64     Cached
  + mtbseq                           1.0.3  pl526_1              bioconda/linux-64          90MB
  + ncurses                            6.3  h27087fc_1           conda-forge/linux-64     Cached
  + openjdk                        8.0.332  h166bdaf_0           conda-forge/linux-64     Cached
  + openssl                         1.1.1s  h0b41bf4_1           conda-forge/linux-64     Cached
  + pango                           1.42.4  h69149e4_5           conda-forge/linux-64     Cached
  + pcre                              8.45  h9c3ff4c_0           conda-forge/linux-64     Cached
  + pcre2                            10.36  h032f7d1_1           conda-forge/linux-64     Cached
  + perl                            5.26.2  h36c2ea0_1008        conda-forge/linux-64     Cached
  + perl-base                         2.23  pl526_1              bioconda/linux-64        Cached
  + perl-carp                         1.38  pl526_3              bioconda/linux-64        Cached
  + perl-constant                     1.33  pl526_1              bioconda/linux-64        Cached
  + perl-exporter                     5.72  pl526_1              bioconda/linux-64        Cached
  + perl-extutils-makemaker           7.36  pl526_1              bioconda/linux-64        Cached
  + perl-file-path                    2.16  pl526_0              bioconda/linux-64        Cached
  + perl-getopt-long                  2.50  pl526_1              bioconda/linux-64        Cached
  + perl-mce                         1.837  pl526_0              bioconda/linux-64        Cached
  + perl-number-format                1.75  pl526_3              bioconda/linux-64        Cached
  + perl-scalar-list-utils            1.52  pl526h516909a_0      bioconda/linux-64        Cached
  + perl-socket                      2.027  pl526_1              bioconda/linux-64        Cached
  + perl-statistics-basic           1.6611  pl526_2              bioconda/linux-64        Cached
  + perl-storable                     3.15  pl526h14c3975_0      bioconda/linux-64        Cached
  + perl-time-hires                 1.9760  pl526h14c3975_1      bioconda/linux-64        Cached
  + perl-xsloader                     0.24  pl526_0              bioconda/linux-64        Cached
  + picard                          2.27.5  hdfd78af_0           bioconda/noarch          Cached
  + pip                             21.3.1  pyhd8ed1ab_0         conda-forge/noarch       Cached
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  + pthread-stubs                      0.4  h36c2ea0_1001        conda-forge/linux-64     Cached
  + python                          3.6.15  hb7a2778_0_cpython   conda-forge/linux-64     Cached
  + python_abi                         3.6  2_cp36m              conda-forge/linux-64     Cached
  + r-base                           4.0.3  hd23ff56_6           conda-forge/linux-64     Cached
  + readline                         8.1.2  h0f457ee_0           conda-forge/linux-64     Cached
  + samtools                           1.6  h9dace67_6           bioconda/linux-64        Cached
  + sed                                4.8  he412f7d_0           conda-forge/linux-64     Cached
  + setuptools                      58.0.4  py36h5fab9bb_2       conda-forge/linux-64     Cached
  + sqlite                          3.40.0  h4ff8645_0           conda-forge/linux-64     Cached
  + sysroot_linux-64                  2.12  he073ed8_15          conda-forge/noarch       Cached
  + tk                              8.6.12  h27826a3_0           conda-forge/linux-64     Cached
  + tktable                           2.10  hb7b940f_3           conda-forge/linux-64     Cached
  + wheel                           0.37.1  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + xorg-kbproto                     1.0.7  h7f98852_1002        conda-forge/linux-64     Cached
  + xorg-libice                     1.0.10  h7f98852_0           conda-forge/linux-64     Cached
  + xorg-libsm                       1.2.3  hd9c2040_1000        conda-forge/linux-64     Cached
  + xorg-libx11                      1.7.2  h7f98852_0           conda-forge/linux-64     Cached
  + xorg-libxau                      1.0.9  h7f98852_0           conda-forge/linux-64     Cached
  + xorg-libxdmcp                    1.1.3  h7f98852_0           conda-forge/linux-64     Cached
  + xorg-libxext                     1.3.4  h7f98852_1           conda-forge/linux-64     Cached
  + xorg-libxrender                 0.9.10  h7f98852_1003        conda-forge/linux-64     Cached
  + xorg-libxt                       1.2.1  h7f98852_2           conda-forge/linux-64     Cached
  + xorg-renderproto                0.11.1  h7f98852_1002        conda-forge/linux-64     Cached
  + xorg-xextproto                   7.3.0  h7f98852_1002        conda-forge/linux-64     Cached
  + xorg-xproto                     7.0.31  h7f98852_1007        conda-forge/linux-64     Cached
  + xz                               5.2.6  h166bdaf_0           conda-forge/linux-64     Cached
  + zlib                            1.2.13  h166bdaf_4           conda-forge/linux-64     Cached
  + zstd                             1.5.2  h3eb15da_6           conda-forge/linux-64     Cached
abhi18av commented 1 year ago

gatk-register works with mtbseq-v1.0.3


$ mamba activate mtbseq-103-env

$ gatk-register GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar

$ MTBseq  --check                                                        (mtbseq-103-env)
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
    LANGUAGE = (unset),
    LC_ALL = (unset),
    LC_CTYPE = "UTF-8",
    LANG = "en_US.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to a fallback locale ("en_US.UTF-8").
<INFO>  [2023-02-06 16:41:36]   Found perl module: MCE
<INFO>  [2023-02-06 16:41:36]   Found perl module: Statistics::Basic
<INFO>  [2023-02-06 16:41:36]   Found bwa in your PATH!
<INFO>  [2023-02-06 16:41:36]   Found samtools in your PATH!
<INFO>  [2023-02-06 16:41:36]   Found gatk in your PATH!
<INFO>  [2023-02-06 16:41:36]   Found picard in your PATH!