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kavonrtep / dante_ltr

GNU General Public License v3.0
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Problem in installing dante_ltr with conda #6

Open mixle18 opened 10 months ago

mixle18 commented 10 months ago

Hi, I am trying to install dante_ltr through conda. The tool is properly installed without any errors. However when I try to execute it as dante_ltr, its showing command not found. Can you help, if this is the problem with an conda update or something else.

conda create -n dante_ltr -c bioconda -c conda-forge -c petrnovak dante_ltr Retrieving notices: ...working... done Collecting package metadata (current_repodata.json): done Solving environment: done

Package Plan

environment location: /home/lab7/Conda/envs/dante_ltr

added / updated specs:

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
argcomplete-3.2.1          |     pyhd8ed1ab_0          39 KB  conda-forge
bioconductor-biobase-2.62.0|    r43ha9d7317_1         2.4 MB  bioconda
bioconductor-biocgenerics-0.48.1|    r43hdfd78af_2         643 KB  bioconda
bioconductor-biocio-1.12.0 |    r43hdfd78af_0         456 KB  bioconda
bioconductor-biocparallel-1.36.0|    r43hf17093f_1         1.6 MB  bioconda
bioconductor-biostrings-2.70.1|    r43ha9d7317_1        13.9 MB  bioconda
bioconductor-bsgenome-1.70.1|    r43hdfd78af_0         7.0 MB  bioconda
bioconductor-data-packages-20231203|       hdfd78af_0         406 KB  bioconda
bioconductor-delayedarray-0.28.0|    r43ha9d7317_1         2.3 MB  bioconda
bioconductor-genomeinfodb-1.38.1|    r43hdfd78af_1         4.2 MB  bioconda
bioconductor-genomeinfodbdata-1.2.11|    r43hdfd78af_1           8 KB  bioconda
bioconductor-genomicalignments-1.38.0|    r43ha9d7317_0         2.4 MB  bioconda
bioconductor-genomicranges-1.54.1|    r43ha9d7317_1         2.2 MB  bioconda
bioconductor-iranges-2.36.0|    r43ha9d7317_1         2.5 MB  bioconda
bioconductor-matrixgenerics-1.14.0|    r43hdfd78af_1         453 KB  bioconda
bioconductor-rhtslib-2.4.0 |    r43ha9d7317_1         2.3 MB  bioconda
bioconductor-rsamtools-2.18.0|    r43hf17093f_1         4.0 MB  bioconda
bioconductor-rtracklayer-1.62.0|    r43ha9d7317_0         5.3 MB  bioconda
bioconductor-s4arrays-1.2.0|    r43ha9d7317_1         795 KB  bioconda
bioconductor-s4vectors-0.40.2|    r43ha9d7317_1         2.4 MB  bioconda
bioconductor-sparsearray-1.2.2|    r43ha9d7317_1         1.6 MB  bioconda
bioconductor-summarizedexperiment-1.32.0|    r43hdfd78af_0         1.9 MB  bioconda
bioconductor-xvector-0.42.0|    r43ha9d7317_1         738 KB  bioconda
bioconductor-zlibbioc-1.48.0|    r43ha9d7317_1          25 KB  bioconda
c-ares-1.25.0              |       hd590300_0         153 KB  conda-forge
dante_ltr-0.1.6.1          |                0        65.1 MB  petrnovak
pyyaml-6.0.1               |  py312h98912ed_1         192 KB  conda-forge
r-abind-1.4_5              | r43hc72bb7e_1005          76 KB  conda-forge
r-bh-1.84.0_0              |    r43hc72bb7e_0        10.9 MB  conda-forge
r-cpp11-0.4.7              |    r43hc72bb7e_0         224 KB  conda-forge
r-getopt-1.20.4            |    r43ha770c72_0          50 KB  conda-forge
r-matrix-1.6_5             |    r43h316c678_0         3.7 MB  conda-forge
r-matrixstats-1.2.0        |    r43h57805ef_0         455 KB  conda-forge
r-rcurl-1.98_1.14          |    r43hf9611b0_0         807 KB  conda-forge
r-xml-3.99_0.16            |    r43hc38eee6_0         1.7 MB  conda-forge
r-yaml-2.3.8               |    r43h57805ef_0         116 KB  conda-forge
------------------------------------------------------------
                                       Total:       143.0 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-4.5-2_gnu _r-mutex conda-forge/noarch::_r-mutex-1.0.1-anacondar_1 argcomplete conda-forge/noarch::argcomplete-3.2.1-pyhd8ed1ab_0 binutils_impl_lin~ conda-forge/linux-64::binutils_impl_linux-64-2.40-hf600244_0 bioconductor-biob~ bioconda/linux-64::bioconductor-biobase-2.62.0-r43ha9d7317_1 bioconductor-bioc~ bioconda/noarch::bioconductor-biocgenerics-0.48.1-r43hdfd78af_2 bioconductor-bioc~ bioconda/noarch::bioconductor-biocio-1.12.0-r43hdfd78af_0 bioconductor-bioc~ bioconda/linux-64::bioconductor-biocparallel-1.36.0-r43hf17093f_1 bioconductor-bios~ bioconda/linux-64::bioconductor-biostrings-2.70.1-r43ha9d7317_1 bioconductor-bsge~ bioconda/noarch::bioconductor-bsgenome-1.70.1-r43hdfd78af_0 bioconductor-data~ bioconda/noarch::bioconductor-data-packages-20231203-hdfd78af_0 bioconductor-dela~ bioconda/linux-64::bioconductor-delayedarray-0.28.0-r43ha9d7317_1 bioconductor-geno~ bioconda/noarch::bioconductor-genomeinfodb-1.38.1-r43hdfd78af_1 bioconductor-geno~ bioconda/noarch::bioconductor-genomeinfodbdata-1.2.11-r43hdfd78af_1 bioconductor-geno~ bioconda/linux-64::bioconductor-genomicalignments-1.38.0-r43ha9d7317_0 bioconductor-geno~ bioconda/linux-64::bioconductor-genomicranges-1.54.1-r43ha9d7317_1 bioconductor-iran~ bioconda/linux-64::bioconductor-iranges-2.36.0-r43ha9d7317_1 bioconductor-matr~ bioconda/noarch::bioconductor-matrixgenerics-1.14.0-r43hdfd78af_1 bioconductor-rhts~ bioconda/linux-64::bioconductor-rhtslib-2.4.0-r43ha9d7317_1 bioconductor-rsam~ bioconda/linux-64::bioconductor-rsamtools-2.18.0-r43hf17093f_1 bioconductor-rtra~ bioconda/linux-64::bioconductor-rtracklayer-1.62.0-r43ha9d7317_0 bioconductor-s4ar~ bioconda/linux-64::bioconductor-s4arrays-1.2.0-r43ha9d7317_1 bioconductor-s4ve~ bioconda/linux-64::bioconductor-s4vectors-0.40.2-r43ha9d7317_1 bioconductor-spar~ bioconda/linux-64::bioconductor-sparsearray-1.2.2-r43ha9d7317_1 bioconductor-summ~ bioconda/noarch::bioconductor-summarizedexperiment-1.32.0-r43hdfd78af_0 bioconductor-xvec~ bioconda/linux-64::bioconductor-xvector-0.42.0-r43ha9d7317_1 bioconductor-zlib~ bioconda/linux-64::bioconductor-zlibbioc-1.48.0-r43ha9d7317_1 blast bioconda/linux-64::blast-2.5.0-hc0b0e79_3 boost conda-forge/linux-64::boost-1.84.0-h8da182e_0 bwidget conda-forge/linux-64::bwidget-1.9.14-ha770c72_1 bzip2 conda-forge/linux-64::bzip2-1.0.8-hd590300_5 c-ares conda-forge/linux-64::c-ares-1.25.0-hd590300_0 ca-certificates conda-forge/linux-64::ca-certificates-2023.11.17-hbcca054_0 cairo conda-forge/linux-64::cairo-1.18.0-h3faef2a_0 curl conda-forge/linux-64::curl-8.5.0-hca28451_0 dante_ltr petrnovak/linux-64::dante_ltr-0.1.6.1-0 expat conda-forge/linux-64::expat-2.5.0-hcb278e6_1 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_1 fontconfig conda-forge/linux-64::fontconfig-2.14.2-h14ed4e7_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-2.12.1-h267a509_2 fribidi conda-forge/linux-64::fribidi-1.0.10-h36c2ea0_0 gcc_impl_linux-64 conda-forge/linux-64::gcc_impl_linux-64-13.2.0-h338b0a0_3 gettext conda-forge/linux-64::gettext-0.21.1-h27087fc_0 gfortran_impl_lin~ conda-forge/linux-64::gfortran_impl_linux-64-13.2.0-h76e1118_3 graphite2 conda-forge/linux-64::graphite2-1.3.13-h58526e2_1001 gxx_impl_linux-64 conda-forge/linux-64::gxx_impl_linux-64-13.2.0-h338b0a0_3 harfbuzz conda-forge/linux-64::harfbuzz-8.3.0-h3d44ed6_0 icu conda-forge/linux-64::icu-73.2-h59595ed_0 jq bioconda/linux-64::jq-1.5-0 kernel-headers_li~ conda-forge/noarch::kernel-headers_linux-64-2.6.32-he073ed8_16 keyutils conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0 krb5 conda-forge/linux-64::krb5-1.21.2-h659d440_0 ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-h41732ed_0 lerc conda-forge/linux-64::lerc-4.0.0-h27087fc_0 libblas conda-forge/linux-64::libblas-3.9.0-20_linux64_openblas libboost conda-forge/linux-64::libboost-1.84.0-h6fcfa73_0 libboost-devel conda-forge/linux-64::libboost-devel-1.84.0-h00ab1b0_0 libboost-headers conda-forge/linux-64::libboost-headers-1.84.0-ha770c72_0 libboost-python conda-forge/linux-64::libboost-python-1.84.0-py312hfb10629_0 libboost-python-d~ conda-forge/linux-64::libboost-python-devel-1.84.0-py312h8da182e_0 libcblas conda-forge/linux-64::libcblas-3.9.0-20_linux64_openblas libcurl conda-forge/linux-64::libcurl-8.5.0-hca28451_0 libdeflate conda-forge/linux-64::libdeflate-1.19-hd590300_0 libedit conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2 libev conda-forge/linux-64::libev-4.33-hd590300_2 libexpat conda-forge/linux-64::libexpat-2.5.0-hcb278e6_1 libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5 libgcc conda-forge/linux-64::libgcc-7.2.0-h69d50b8_2 libgcc-devel_linu~ conda-forge/noarch::libgcc-devel_linux-64-13.2.0-ha9c7c90_103 libgcc-ng conda-forge/linux-64::libgcc-ng-13.2.0-h807b86a_3 libgfortran-ng conda-forge/linux-64::libgfortran-ng-13.2.0-h69a702a_3 libgfortran5 conda-forge/linux-64::libgfortran5-13.2.0-ha4646dd_3 libglib conda-forge/linux-64::libglib-2.78.3-h783c2da_0 libgomp conda-forge/linux-64::libgomp-13.2.0-h807b86a_3 libiconv conda-forge/linux-64::libiconv-1.17-hd590300_2 libjpeg-turbo conda-forge/linux-64::libjpeg-turbo-3.0.0-hd590300_1 liblapack conda-forge/linux-64::liblapack-3.9.0-20_linux64_openblas libnghttp2 conda-forge/linux-64::libnghttp2-1.58.0-h47da74e_1 libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0 libopenblas conda-forge/linux-64::libopenblas-0.3.25-pthreads_h413a1c8_0 libpng conda-forge/linux-64::libpng-1.6.39-h753d276_0 libsanitizer conda-forge/linux-64::libsanitizer-13.2.0-h7e041cc_3 libsqlite conda-forge/linux-64::libsqlite-3.44.2-h2797004_0 libssh2 conda-forge/linux-64::libssh2-1.11.0-h0841786_0 libstdcxx-devel_l~ conda-forge/noarch::libstdcxx-devel_linux-64-13.2.0-ha9c7c90_103 libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-13.2.0-h7e041cc_3 libtiff conda-forge/linux-64::libtiff-4.6.0-ha9c0a0a_2 libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0 libwebp-base conda-forge/linux-64::libwebp-base-1.3.2-hd590300_0 libxcb conda-forge/linux-64::libxcb-1.15-h0b41bf4_0 libxcrypt conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1 libxml2 conda-forge/linux-64::libxml2-2.11.6-h232c23b_0 libzlib conda-forge/linux-64::libzlib-1.2.13-hd590300_5 make conda-forge/linux-64::make-4.3-hd18ef5c_1 ncurses conda-forge/linux-64::ncurses-6.4-h59595ed_2 numpy conda-forge/linux-64::numpy-1.26.3-py312heda63a1_0 openssl conda-forge/linux-64::openssl-3.2.0-hd590300_1 pango conda-forge/linux-64::pango-1.50.14-ha41ecd1_2 pcre2 conda-forge/linux-64::pcre2-10.42-hcad00b1_0 pip conda-forge/noarch::pip-23.3.2-pyhd8ed1ab_0 pixman conda-forge/linux-64::pixman-0.43.0-h59595ed_0 pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-h36c2ea0_1001 python conda-forge/linux-64::python-3.12.1-hab00c5b_1_cpython python_abi conda-forge/linux-64::python_abi-3.12-4_cp312 pyyaml conda-forge/linux-64::pyyaml-6.0.1-py312h98912ed_1 r-abind conda-forge/noarch::r-abind-1.4_5-r43hc72bb7e_1005 r-base conda-forge/linux-64::r-base-4.3.2-hb8ee39d_1 r-bh conda-forge/noarch::r-bh-1.84.0_0-r43hc72bb7e_0 r-bitops conda-forge/linux-64::r-bitops-1.0_7-r43h57805ef_2 r-codetools conda-forge/noarch::r-codetools-0.2_19-r43hc72bb7e_1 r-cpp11 conda-forge/noarch::r-cpp11-0.4.7-r43hc72bb7e_0 r-crayon conda-forge/noarch::r-crayon-1.5.2-r43hc72bb7e_2 r-formatr conda-forge/noarch::r-formatr-1.14-r43hc72bb7e_1 r-futile.logger conda-forge/noarch::r-futile.logger-1.4.3-r43hc72bb7e_1005 r-futile.options conda-forge/noarch::r-futile.options-1.0.1-r43hc72bb7e_1004 r-getopt conda-forge/noarch::r-getopt-1.20.4-r43ha770c72_0 r-lambda.r conda-forge/noarch::r-lambda.r-1.2.4-r43hc72bb7e_3 r-lattice conda-forge/linux-64::r-lattice-0.22_5-r43h57805ef_0 r-matrix conda-forge/linux-64::r-matrix-1.6_5-r43h316c678_0 r-matrixstats conda-forge/linux-64::r-matrixstats-1.2.0-r43h57805ef_0 r-optparse conda-forge/noarch::r-optparse-1.7.3-r43hc72bb7e_2 r-rcurl conda-forge/linux-64::r-rcurl-1.98_1.14-r43hf9611b0_0 r-restfulr bioconda/linux-64::r-restfulr-0.0.15-r43h56115f1_3 r-rjson conda-forge/linux-64::r-rjson-0.2.21-r43ha503ecb_3 r-snow conda-forge/noarch::r-snow-0.4_4-r43hc72bb7e_2 r-xml conda-forge/linux-64::r-xml-3.99_0.16-r43hc38eee6_0 r-yaml conda-forge/linux-64::r-yaml-2.3.8-r43h57805ef_0 readline conda-forge/linux-64::readline-8.2-h8228510_1 sed conda-forge/linux-64::sed-4.8-he412f7d_0 setuptools conda-forge/noarch::setuptools-69.0.3-pyhd8ed1ab_0 sysroot_linux-64 conda-forge/noarch::sysroot_linux-64-2.12-he073ed8_16 tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 tktable conda-forge/linux-64::tktable-2.10-h0c5db8f_5 toml conda-forge/noarch::toml-0.10.2-pyhd8ed1ab_0 tomlkit conda-forge/noarch::tomlkit-0.12.3-pyha770c72_0 tzdata conda-forge/noarch::tzdata-2023d-h0c530f3_0 wheel conda-forge/noarch::wheel-0.42.0-pyhd8ed1ab_0 xmltodict conda-forge/noarch::xmltodict-0.13.0-pyhd8ed1ab_0 xorg-kbproto conda-forge/linux-64::xorg-kbproto-1.0.7-h7f98852_1002 xorg-libice conda-forge/linux-64::xorg-libice-1.1.1-hd590300_0 xorg-libsm conda-forge/linux-64::xorg-libsm-1.2.4-h7391055_0 xorg-libx11 conda-forge/linux-64::xorg-libx11-1.8.7-h8ee46fc_0 xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.11-hd590300_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-h0b41bf4_2 xorg-libxrender conda-forge/linux-64::xorg-libxrender-0.9.11-hd590300_0 xorg-libxt conda-forge/linux-64::xorg-libxt-1.3.0-hd590300_1 xorg-renderproto conda-forge/linux-64::xorg-renderproto-0.11.1-h7f98852_1002 xorg-xextproto conda-forge/linux-64::xorg-xextproto-7.3.0-h0b41bf4_1003 xorg-xproto conda-forge/linux-64::xorg-xproto-7.0.31-h7f98852_1007 xz conda-forge/linux-64::xz-5.2.6-h166bdaf_0 yaml conda-forge/linux-64::yaml-0.2.5-h7f98852_2 yq conda-forge/noarch::yq-3.2.3-pyhd8ed1ab_0 zlib conda-forge/linux-64::zlib-1.2.13-hd590300_5 zstd conda-forge/linux-64::zstd-1.5.5-hfc55251_0

Proceed ([y]/n)? y

Downloading and Extracting Packages

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

To activate this environment, use

$ conda activate dante_ltr

To deactivate an active environment, use

$ conda deactivate

(dante_ltr) lab7@lab7:~$ dante_ltr
dante_ltr: command not found

Thank You

kavonrtep commented 10 months ago

it seem it installed some old version, try specify version using:

conda create -n dante_ltr -c bioconda -c conda-forge -c petrnovak dante_ltr=0.3.5.0
mixle18 commented 8 months ago

it still not installing.

kavonrtep commented 8 months ago

I need more information can you show me please complete log you get when you install dante_ltr with command: conda create -n dante_ltr -c bioconda -c conda-forge -c petrnovak dante_ltr=0.3.5.0

After install what you get if you run these commands?:

conda activate dante_ltr
ls $CONDA_PREFIX/bin -lL
mankiddyman commented 6 days ago

i had some trouble using micromamba today, i was able to get version 0.4.0.5 using

micromamba create env dante_ltr

micromamba install petrnovak::dante_ltr