Closed abhi18av closed 2 years ago
Na, still runs across the same problem 🤷
Continuation of the saga https://github.com/mtb-bioinformatics/mtbseq-nf/issues/54
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 🔴
Hmm, now the transition to mtbseq-1.0.4
might actually be possible!
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.
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
Create the env and download the bioconda package
mamba create -n mtbseq-env -c bioconda mtbseq
Download the GATK jar
$ wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2
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
==============
$ 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'
$ 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
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!
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
v-1.0.3
$ 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
+ 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
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!
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