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conda-forge / quarto-feedstock

A conda-smithy repository for quarto.
BSD 3-Clause "New" or "Revised" License
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`quarto: deno: No such file or directory` #29

Closed idot closed 1 year ago

idot commented 1 year ago

Solution to issue cannot be found in the documentation.

Issue

Installing with conda both on a real computer and Singularity deno is not found when executing quarto. The script quarto expects deno in the wrong place. It is installed right there next to the quarto script. Hardcoding the deno path in line 158 fixes the problem (but is of course not what conda needs as a script).

real computer

❯ quarto
/users/ido.tamir/.conda/envs/mamba/envs/bioinfo/bin/quarto: line 158: /users/ido.tamir/.conda/envs/mamba/envs/bioinfo/bin/tools/deno-x86_64-unknown-linux-gnu/deno: No such file or directory
❯ find /users/ido.tamir/.conda/envs/mamba/envs/bioinfo -name "deno"
/users/ido.tamir/.conda/envs/mamba/envs/bioinfo/pkgs/quarto-1.3.450-ha770c72_0/bin/vendor/deno-land/x/puppeteer@9-0-2/src/deno
/users/ido.tamir/.conda/envs/mamba/envs/bioinfo/pkgs/deno-1.28.2-h2f28480_0/bin/deno
/users/ido.tamir/.conda/envs/mamba/envs/bioinfo/bin/deno
/users/ido.tamir/.conda/envs/mamba/envs/bioinfo/bin/vendor/deno-land/x/puppeteer@9-0-2/src/deno

Singularity:

Singularity> quarto
/opt/conda/envs/bio/bin/quarto: line 158: /opt/conda/envs/bio/bin/tools/deno-x86_64-unknown-linux-gnu/deno: No such file or directory
Singularity>
Singularity> which quarto
/opt/conda/envs/bio/bin/quarto
Singularity> find /opt/conda/envs/bio -name "*deno*"
/opt/conda/envs/bio/bin/deno
/opt/conda/envs/bio/bin/vendor/deno-land
/opt/conda/envs/bio/bin/vendor/deno-land/x/puppeteer@9-0-2/src/deno
/opt/conda/envs/bio/bin/vendor/deno-land/x/puppeteer@9-0-2/src/initialize-deno.ts
/opt/conda/envs/bio/bin/vendor/import_map_deno_vendor.json
/opt/conda/envs/bio/conda-meta/deno-1.28.2-h2f28480_0.json
/opt/conda/envs/bio/conda-meta/deno-dom-0.1.35-hd9586b0_1.json
/opt/conda/envs/bio/etc/conda/activate.d/deno.sh
/opt/conda/envs/bio/etc/conda/activate.d/deno_dom.sh
/opt/conda/envs/bio/etc/conda/deactivate.d/deno.sh
/opt/conda/envs/bio/etc/conda/deactivate.d/deno_dom.sh
/opt/conda/envs/bio/lib/deno_dom.so
/opt/conda/envs/bio/share/quarto/conf/deno-ts-compile.jsonc
/opt/conda/envs/bio/share/quarto/conf/deno.lock
/opt/conda/envs/bio/share/quarto/deno_std
/opt/conda/envs/bio/share/quarto/deno_std/cache/deps/https/deno.land
/opt/conda/envs/bio/share/quarto/deno_std/cache/gen/file/home/conda/feedstock_root/build_artifacts/quarto_1691275308296/work/package/scripts/deno_std
/opt/conda/envs/bio/share/quarto/deno_std/cache/gen/file/home/conda/feedstock_root/build_artifacts/quarto_1691275308296/work/package/scripts/deno_std/deno_std.ts.js
/opt/conda/envs/bio/share/quarto/deno_std/cache/gen/file/home/conda/feedstock_root/build_artifacts/quarto_1691275308296/work/package/scripts/deno_std/deno_std.ts.meta
/opt/conda/envs/bio/share/quarto/deno_std/cache/gen/https/deno.land
/opt/conda/envs/bio/share/quarto/deno_std/deno_std.lock

Installed packages

❯ conda list
# packages in environment at /users/ido.tamir/.conda/envs/mamba/envs/bioinfo:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                  2_kmp_llvm    conda-forge
_r-mutex                  1.0.1               anacondar_1    conda-forge
alsa-lib                  1.2.6.1              h7f98852_0    conda-forge
argcomplete               3.0.5              pyhd8ed1ab_0    conda-forge
atk                       2.38.0               ha770c72_1    conda-forge
atk-1.0                   2.38.0               hd4edc92_1    conda-forge
attmap                    0.13.2             pyhd8ed1ab_0    conda-forge
attr                      2.5.1                h166bdaf_1    conda-forge
attrs                     22.2.0             pyh71513ae_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.12.2                   pypi_0    pypi
bedtools                  2.30.0               h468198e_3    bioconda
binutils_impl_linux-64    2.40                 hf600244_0    conda-forge
bioconductor-annotationdbi 1.60.0            r42hdfd78af_0    bioconda
bioconductor-biobase      2.58.0            r42hc0cfd56_0    bioconda
bioconductor-biocfilecache 2.6.0             r42hdfd78af_0    bioconda
bioconductor-biocgenerics 0.44.0            r42hdfd78af_0    bioconda
bioconductor-biocio       1.8.0             r42hdfd78af_0    bioconda
bioconductor-biocparallel 1.32.5            r42hc247a5b_0    bioconda
bioconductor-biomart      2.54.0            r42hdfd78af_0    bioconda
bioconductor-biostrings   2.66.0            r42hc0cfd56_0    bioconda
bioconductor-data-packages 20230202             hdfd78af_0    bioconda
bioconductor-delayedarray 0.24.0            r42hc0cfd56_0    bioconda
bioconductor-dupradar     1.28.0            r42hdfd78af_0    bioconda
bioconductor-genomeinfodb 1.34.8            r42hdfd78af_0    bioconda
bioconductor-genomeinfodbdata 1.2.9             r42hdfd78af_0    bioconda
bioconductor-genomicalignments 1.34.0            r42hc0cfd56_0    bioconda
bioconductor-genomicfeatures 1.50.2            r42hdfd78af_0    bioconda
bioconductor-genomicranges 1.50.0            r42hc0cfd56_0    bioconda
bioconductor-iranges      2.32.0            r42hc0cfd56_0    bioconda
bioconductor-keggrest     1.38.0            r42hdfd78af_0    bioconda
bioconductor-matrixgenerics 1.10.0            r42hdfd78af_0    bioconda
bioconductor-rhtslib      2.0.0             r42hc0cfd56_0    bioconda
bioconductor-rsamtools    2.14.0            r42hc247a5b_0    bioconda
bioconductor-rsubread     2.12.0            r42hc0cfd56_0    bioconda
bioconductor-rtracklayer  1.58.0            r42h171f361_1    bioconda
bioconductor-s4vectors    0.36.0            r42hc0cfd56_0    bioconda
bioconductor-summarizedexperiment 1.28.0            r42hdfd78af_0    bioconda
bioconductor-xvector      0.38.0            r42hc0cfd56_0    bioconda
bioconductor-zlibbioc     1.44.0            r42hc0cfd56_0    bioconda
biopython                 1.81            py310h1fa729e_0    conda-forge
blas                      2.116                  openblas    conda-forge
blas-devel                3.9.0           16_linux64_openblas    conda-forge
blast                     2.13.0               hf3cf87c_0    bioconda
bleach                    6.0.0              pyhd8ed1ab_0    conda-forge
bokeh                     3.2.0                    pypi_0    pypi
boltons                   23.0.0             pyhd8ed1ab_0    conda-forge
brotli                    1.0.9                h166bdaf_8    conda-forge
brotli-bin                1.0.9                h166bdaf_8    conda-forge
brotlipy                  0.7.0           py310h5764c6d_1005    conda-forge
bs4                       0.0.1                    pypi_0    pypi
bwidget                   1.9.14               ha770c72_1    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2023.7.22            hbcca054_0    conda-forge
cairo                     1.16.0            ha61ee94_1014    conda-forge
cattrs                    22.2.0             pyhd8ed1ab_0    conda-forge
cd-hit                    4.8.1                h5b5514e_7    bioconda
certifi                   2023.7.22          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1          py310h255011f_3    conda-forge
cfgv                      3.3.1              pyhd8ed1ab_0    conda-forge
chardet                   5.1.0           py310hff52083_0    conda-forge
charset-normalizer        2.1.1              pyhd8ed1ab_0    conda-forge
cheetah3                  3.2.6.post2     py310h5764c6d_3    conda-forge
click                     8.1.3           unix_pyhd8ed1ab_2    conda-forge
click-log                 0.4.0              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
coloredlogs               15.0.1             pyhd8ed1ab_3    conda-forge
colormath                 3.0.0                      py_2    conda-forge
conda                     23.7.2          py310hff52083_0    conda-forge
conda-package-handling    2.0.2              pyh38be061_0    conda-forge
conda-package-streaming   0.7.0              pyhd8ed1ab_1    conda-forge
contourpy                 1.0.7           py310hdf3cbec_0    conda-forge
cryptography              39.0.0          py310h65dfdc0_0    conda-forge
curl                      7.86.0               h7bff187_1    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
dart-sass                 1.58.3               ha770c72_1    conda-forge
dbus                      1.13.6               h5008d03_3    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
deno                      1.28.2               h2f28480_0    conda-forge
deno-dom                  0.1.35               hd9586b0_1    conda-forge
distlib                   0.3.6              pyhd8ed1ab_0    conda-forge
docutils                  0.19            py310hff52083_1    conda-forge
emboss                    6.6.0                h86d058a_5    bioconda
entrez-direct             16.2                 he881be0_1    bioconda
esbuild                   0.15.5               ha770c72_1    conda-forge
exceptiongroup            1.1.1              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                h27087fc_0    conda-forge
fastqc                    0.12.1               hdfd78af_0    bioconda
fftw                      3.3.10          nompi_hf0379b8_106    conda-forge
filelock                  3.10.6             pyhd8ed1ab_0    conda-forge
filetype                  1.2.0              pyhd8ed1ab_0    conda-forge
fmt                       9.1.0                h924138e_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.2               h14ed4e7_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.39.2          py310h1fa729e_0    conda-forge
forskalle-api             1.1.0                    pypi_0    pypi
freetype                  2.12.1               hca18f0e_1    conda-forge
fribidi                   1.0.10               h36c2ea0_0    conda-forge
future                    0.18.3             pyhd8ed1ab_0    conda-forge
galaxy-containers         22.1.1             pyhd8ed1ab_0    conda-forge
galaxy-tool-util          22.1.5             pyhd8ed1ab_0    conda-forge
galaxy-util               22.1.1             pyhd8ed1ab_0    conda-forge
gcc_impl_linux-64         12.2.0              hcc96c02_19    conda-forge
gdk-pixbuf                2.42.8               hff1cb4f_1    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
gfortran_impl_linux-64    12.2.0              h55be85b_19    conda-forge
ghostscript               9.54.0               h27087fc_2    conda-forge
giflib                    5.2.1                h0b41bf4_3    conda-forge
git                       2.38.1          pl5321h5fbbf19_0    conda-forge
gitdb                     4.0.10             pyhd8ed1ab_0    conda-forge
gitdb2                    4.0.2                      py_0    conda-forge
gitpython                 3.1.31             pyhd8ed1ab_0    conda-forge
glib                      2.74.1               h6239696_0    conda-forge
glib-tools                2.74.1               h6239696_0    conda-forge
glpk                      5.0                  h445213a_0    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
graphite2                 1.3.13            h58526e2_1001    conda-forge
graphviz                  6.0.2                h99bc08f_0    conda-forge
gsl                       2.7                  he838d99_0    conda-forge
gst-plugins-base          1.20.3               hf6a322e_0    conda-forge
gstreamer                 1.20.3               hd4edc92_2    conda-forge
gtk2                      2.24.33              h90689f9_2    conda-forge
gts                       0.7.6                h64030ff_2    conda-forge
gxx_impl_linux-64         12.2.0              hcc96c02_19    conda-forge
harfbuzz                  6.0.0                h8e241bc_0    conda-forge
hdf5                      1.12.2          nompi_h2386368_100    conda-forge
htslib                    1.16                 h6bc39ce_0    bioconda
humanfriendly             10.0            py310hff52083_4    conda-forge
icu                       70.1                 h27087fc_0    conda-forge
identify                  2.5.22             pyhd8ed1ab_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
illumina-interop          1.2.2                h87f3376_0    bioconda
imagemagick               7.1.0_50        pl5321hbb10140_0    conda-forge
importlib-metadata        6.1.0              pyha770c72_0    conda-forge
importlib_resources       5.12.0             pyhd8ed1ab_0    conda-forge
iniconfig                 2.0.0              pyhd8ed1ab_0    conda-forge
itsdangerous              2.1.2              pyhd8ed1ab_0    conda-forge
jack                      1.9.18            h8c3723f_1002    conda-forge
jbig                      2.1               h7f98852_2003    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
jpeg                      9e                   h0b41bf4_3    conda-forge
jq                        1.6               h36c2ea0_1000    conda-forge
jsonpatch                 1.32               pyhd8ed1ab_0    conda-forge
jsonpointer               2.0                        py_0    conda-forge
jsonschema                4.17.3             pyhd8ed1ab_0    conda-forge
kernel-headers_linux-64   2.6.32              he073ed8_15    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.4           py310hbf28c38_1    conda-forge
krb5                      1.19.3               h3790be6_0    conda-forge
lcms2                     2.14                 h6ed2654_0    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libarchive                3.5.2                hb890918_3    conda-forge
libblas                   3.9.0           16_linux64_openblas    conda-forge
libbrotlicommon           1.0.9                h166bdaf_8    conda-forge
libbrotlidec              1.0.9                h166bdaf_8    conda-forge
libbrotlienc              1.0.9                h166bdaf_8    conda-forge
libcap                    2.64                 ha37c62d_0    conda-forge
libcblas                  3.9.0           16_linux64_openblas    conda-forge
libclang                  14.0.6          default_h2e3cab8_0    conda-forge
libclang13                14.0.6          default_h3a83d3e_0    conda-forge
libcups                   2.3.3                h3e49a29_2    conda-forge
libcurl                   7.86.0               h7bff187_1    conda-forge
libdb                     6.2.32               h9c3ff4c_0    conda-forge
libdeflate                1.13                 h166bdaf_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libevent                  2.1.10               h9b69904_4    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libflac                   1.3.4                h27087fc_0    conda-forge
libgcc-devel_linux-64     12.2.0              h3b97bd3_19    conda-forge
libgcc-ng                 12.2.0              h65d4601_19    conda-forge
libgd                     2.3.3                h18fbbfe_3    conda-forge
libgfortran-ng            12.2.0              h69a702a_19    conda-forge
libgfortran5              12.2.0              h337968e_19    conda-forge
libgit2                   1.5.0                h6529ace_0    conda-forge
libglib                   2.74.1               h7a41b64_0    conda-forge
libgomp                   12.2.0              h65d4601_19    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
libidn11                  1.34                 h1cef754_0    conda-forge
libidn2                   2.3.4                h166bdaf_0    conda-forge
liblapack                 3.9.0           16_linux64_openblas    conda-forge
liblapacke                3.9.0           16_linux64_openblas    conda-forge
libllvm14                 14.0.6               he0ac6c6_1    conda-forge
libmamba                  0.24.0               hd8a31e3_1    conda-forge
libmambapy                0.24.0          py310hab0e683_1    conda-forge
libnghttp2                1.51.0               hdcd2b5c_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libogg                    1.3.4                h7f98852_1    conda-forge
libopenblas               0.3.21          pthreads_h78a6416_3    conda-forge
libopus                   1.3.1                h7f98852_1    conda-forge
libpng                    1.6.39               h753d276_0    conda-forge
libpq                     14.5                 h72a31a5_3    conda-forge
librsvg                   2.54.4               h7abd40a_0    conda-forge
libsanitizer              12.2.0              h46fd767_19    conda-forge
libsndfile                1.0.31               h9c3ff4c_1    conda-forge
libsolv                   0.7.23               h3eb15da_0    conda-forge
libsqlite                 3.40.0               h753d276_0    conda-forge
libssh2                   1.10.0               haa6b8db_3    conda-forge
libstdcxx-devel_linux-64  12.2.0              h3b97bd3_19    conda-forge
libstdcxx-ng              12.2.0              h46fd767_19    conda-forge
libtiff                   4.4.0                h0e0dad5_3    conda-forge
libtool                   2.4.7                h27087fc_0    conda-forge
libudev1                  253                  h0b41bf4_0    conda-forge
libunistring              0.9.10               h7f98852_0    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libvorbis                 1.3.7                h9c3ff4c_0    conda-forge
libwebp                   1.2.4                h522a892_0    conda-forge
libwebp-base              1.2.4                h166bdaf_0    conda-forge
libxcb                    1.13              h7f98852_1004    conda-forge
libxkbcommon              1.0.3                he3ba5ed_0    conda-forge
libxml2                   2.9.14               h22db469_4    conda-forge
libxslt                   1.1.35               h8affb1d_0    conda-forge
libzlib                   1.2.13               h166bdaf_4    conda-forge
llvm-openmp               16.0.0               h417c0b6_0    conda-forge
logmuse                   0.2.6              pyh8c360ce_0    conda-forge
lxml                      4.9.1           py310h5764c6d_0    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
lzstring                  1.0.4                   py_1001    conda-forge
make                      4.3                  hd18ef5c_1    conda-forge
mamba                     0.24.0          py310hf87f941_1    conda-forge
markdown                  3.4.3              pyhd8ed1ab_0    conda-forge
markdown-it-py            2.2.0              pyhd8ed1ab_0    conda-forge
markupsafe                2.1.2           py310h1fa729e_0    conda-forge
matplotlib                3.7.1           py310hff52083_0    conda-forge
matplotlib-base           3.7.1           py310he60537e_0    conda-forge
mdurl                     0.1.0              pyhd8ed1ab_0    conda-forge
multiqc                   1.14               pyhdfd78af_0    bioconda
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
muscle                    5.1                  h9f5acd7_1    bioconda
mysql-common              8.0.32               h14678bc_0    conda-forge
mysql-libs                8.0.32               h54cf53e_0    conda-forge
ncbi-ngs-sdk              2.9.0                         0    bioconda
ncbi-vdb                  3.0.2                h87f3376_0    bioconda
ncurses                   6.3                  h27087fc_1    conda-forge
networkx                  3.0                pyhd8ed1ab_0    conda-forge
nf-core                   2.9                      pypi_0    pypi
nnn                       4.7                  h40d3029_0    conda-forge
nodeenv                   1.7.0              pyhd8ed1ab_0    conda-forge
nspr                      4.35                 h27087fc_0    conda-forge
nss                       3.89                 he45b914_0    conda-forge
numpy                     1.24.2          py310h8deb116_0    conda-forge
oniguruma                 6.9.8                h166bdaf_0    conda-forge
openblas                  0.3.21          pthreads_h320a7e8_3    conda-forge
openjdk                   11.0.1            h516909a_1016    conda-forge
openjpeg                  2.5.0                h7d73246_1    conda-forge
openssl                   1.1.1v               hd590300_0    conda-forge
ossuuid                   1.6.2             hf484d3e_1000    conda-forge
oyaml                     1.0                pyhd8ed1ab_0    conda-forge
packaging                 23.1               pyhd8ed1ab_0    conda-forge
pandas                    1.5.3           py310h9b08913_0    conda-forge
pandoc                    3.1.1                h32600fe_0    conda-forge
pango                     1.50.14              hd33c08f_0    conda-forge
pcre                      8.45                 h9c3ff4c_0    conda-forge
pcre2                     10.37                hc3806b6_1    conda-forge
perl                      5.32.1          2_h7f98852_perl5    conda-forge
perl-alien-build          2.48            pl5321hec16e2b_0    bioconda
perl-alien-libxml2        0.17            pl5321hec16e2b_0    bioconda
perl-app-cpanminus        1.7046          pl5321hd8ed1ab_0    conda-forge
perl-archive-tar          2.40            pl5321hdfd78af_0    bioconda
perl-base                 2.23            pl5321hd8ed1ab_0    conda-forge
perl-business-isbn        3.007           pl5321hd8ed1ab_0    conda-forge
perl-business-isbn-data   20210112.006    pl5321hd8ed1ab_0    conda-forge
perl-capture-tiny         0.48            pl5321ha770c72_1    conda-forge
perl-carp                 1.50            pl5321hd8ed1ab_0    conda-forge
perl-common-sense         3.75            pl5321hd8ed1ab_0    conda-forge
perl-compress-raw-bzip2   2.201           pl5321h166bdaf_0    conda-forge
perl-compress-raw-zlib    2.202           pl5321h166bdaf_0    conda-forge
perl-constant             1.33            pl5321hd8ed1ab_0    conda-forge
perl-data-dumper          2.183           pl5321h166bdaf_0    conda-forge
perl-digest-hmac          1.04            pl5321hdfd78af_0    bioconda
perl-digest-md5           2.58            pl5321h166bdaf_0    conda-forge
perl-encode               3.19            pl5321h166bdaf_0    conda-forge
perl-encode-locale        1.05            pl5321hdfd78af_7    bioconda
perl-exporter             5.74            pl5321hd8ed1ab_0    conda-forge
perl-exporter-tiny        1.002002        pl5321hd8ed1ab_0    conda-forge
perl-extutils-makemaker   7.70            pl5321hd8ed1ab_0    conda-forge
perl-ffi-checklib         0.28            pl5321hdfd78af_0    bioconda
perl-file-chdir           0.1011          pl5321hd8ed1ab_0    conda-forge
perl-file-listing         6.15            pl5321hdfd78af_0    bioconda
perl-file-path            2.18            pl5321hd8ed1ab_0    conda-forge
perl-file-spec            3.48_01         pl5321hdfd78af_2    bioconda
perl-file-temp            0.2304          pl5321hd8ed1ab_0    conda-forge
perl-file-which           1.24            pl5321hd8ed1ab_0    conda-forge
perl-html-parser          3.80            pl5321h9f5acd7_0    bioconda
perl-html-tagset          3.20            pl5321hdfd78af_4    bioconda
perl-html-tree            5.07            pl5321hdfd78af_2    bioconda
perl-http-cookies         6.10            pl5321hdfd78af_0    bioconda
perl-http-daemon          6.15            pl5321hdfd78af_0    bioconda
perl-http-date            6.05            pl5321hdfd78af_0    bioconda
perl-http-message         6.36            pl5321hdfd78af_0    bioconda
perl-http-negotiate       6.01            pl5321hdfd78af_4    bioconda
perl-importer             0.026           pl5321hd8ed1ab_0    conda-forge
perl-io-compress          2.201           pl5321h87f3376_0    bioconda
perl-io-html              1.004           pl5321hdfd78af_0    bioconda
perl-io-socket-ssl        2.075           pl5321hd8ed1ab_0    conda-forge
perl-io-zlib              1.14            pl5321hdfd78af_0    bioconda
perl-json                 4.10            pl5321hdfd78af_0    bioconda
perl-json-xs              2.34            pl5321h9f5acd7_5    bioconda
perl-libwww-perl          6.67            pl5321hdfd78af_0    bioconda
perl-list-moreutils       0.430           pl5321hdfd78af_0    bioconda
perl-list-moreutils-xs    0.430           pl5321hec16e2b_1    bioconda
perl-lwp-mediatypes       6.04            pl5321hdfd78af_1    bioconda
perl-lwp-protocol-https   6.10            pl5321hdfd78af_0    bioconda
perl-mime-base64          3.16            pl5321h166bdaf_0    conda-forge
perl-mozilla-ca           20211001        pl5321hdfd78af_0    bioconda
perl-net-http             6.22            pl5321hdfd78af_0    bioconda
perl-net-ssleay           1.92            pl5321haa6b8db_1    conda-forge
perl-ntlm                 1.09            pl5321hdfd78af_5    bioconda
perl-parent               0.241           pl5321hd8ed1ab_0    conda-forge
perl-path-tiny            0.124           pl5321hd8ed1ab_0    conda-forge
perl-pathtools            3.75            pl5321h166bdaf_0    conda-forge
perl-scalar-list-utils    1.63            pl5321h166bdaf_0    conda-forge
perl-scope-guard          0.21            pl5321hd8ed1ab_0    conda-forge
perl-socket               2.027           pl5321hec16e2b_3    bioconda
perl-storable             3.15            pl5321h166bdaf_0    conda-forge
perl-sub-info             0.002           pl5321hd8ed1ab_0    conda-forge
perl-term-table           0.016           pl5321hdfd78af_0    bioconda
perl-test-fatal           0.016           pl5321ha770c72_0    conda-forge
perl-test-requiresinternet 0.05            pl5321hdfd78af_1    bioconda
perl-test-warnings        0.031           pl5321ha770c72_0    conda-forge
perl-test2-suite          0.000145        pl5321hdfd78af_0    bioconda
perl-time-local           1.30            pl5321hdfd78af_0    bioconda
perl-timedate             2.33            pl5321hdfd78af_2    bioconda
perl-try-tiny             0.31            pl5321ha770c72_0    conda-forge
perl-types-serialiser     1.01            pl5321hdfd78af_0    bioconda
perl-uri                  5.17            pl5321ha770c72_0    conda-forge
perl-url-encode           0.03            pl5321h9ee0642_0    bioconda
perl-www-robotrules       6.02            pl5321hdfd78af_4    bioconda
perl-xml-libxml           2.0207          pl5321h661654b_0    bioconda
perl-xml-namespacesupport 1.12            pl5321hd8ed1ab_0    conda-forge
perl-xml-parser           2.44_01         pl5321hc3e0081_1003    conda-forge
perl-xml-sax              1.02            pl5321hd8ed1ab_0    conda-forge
perl-xml-sax-base         1.09            pl5321hd8ed1ab_0    conda-forge
perl-xml-sax-expat        0.51            pl5321hd8ed1ab_0    conda-forge
perl-xml-simple           2.25            pl5321hdfd78af_2    bioconda
perl-xsloader             0.24            pl5321hd8ed1ab_0    conda-forge
phylip                    3.697                h470a237_0    bioconda
pillow                    9.2.0           py310h454ad03_3    conda-forge
pip                       23.0.1             pyhd8ed1ab_0    conda-forge
piper                     0.12.3             pyhdfd78af_0    bioconda
pixman                    0.40.0               h36c2ea0_0    conda-forge
pkg-config                0.29.2            h36c2ea0_1008    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
platformdirs              3.2.0              pyhd8ed1ab_0    conda-forge
pluggy                    1.0.0              pyhd8ed1ab_5    conda-forge
ply                       3.11                       py_1    conda-forge
pooch                     1.7.0              pyha770c72_3    conda-forge
portaudio                 19.6.0               h57a0ea0_5    conda-forge
pre-commit                3.2.0              pyha770c72_0    conda-forge
presto                    0.7.1              pyhdfd78af_0    bioconda
prompt-toolkit            3.0.38             pyha770c72_0    conda-forge
prompt_toolkit            3.0.38               hd8ed1ab_0    conda-forge
psutil                    5.9.4           py310h5764c6d_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
pulseaudio                14.0                 h7f54b18_8    conda-forge
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycosat                   0.6.4           py310h5764c6d_1    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pycryptodome              3.16.0          py310h1419917_0    conda-forge
pydantic                  1.10.7          py310h1fa729e_0    conda-forge
pyfaidx                   0.7.2.1            pyh7cba7a3_1    bioconda
pygments                  2.14.0             pyhd8ed1ab_0    conda-forge
pyopenssl                 23.1.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyqt                      5.15.7          py310h29803b5_0    conda-forge
pyqt5-sip                 12.11.0         py310hd8f1fbe_0    conda-forge
pyqtchart                 5.15.7          py310h29803b5_0    conda-forge
pyqtwebengine             5.15.7          py310h29803b5_0    conda-forge
pyrsistent                0.19.3          py310h1fa729e_0    conda-forge
pysam                     0.20.0          py310hff46b53_0    bioconda
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
pytest                    7.2.2              pyhd8ed1ab_0    conda-forge
pytest-workflow           2.0.1              pyhd8ed1ab_0    conda-forge
python                    3.10.8          h257c98d_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-slugify            8.0.1              pyhd8ed1ab_0    conda-forge
python_abi                3.10                    3_cp310    conda-forge
pytz                      2023.2             pyhd8ed1ab_0    conda-forge
pyvcf3                    1.0.3              pyhdfd78af_0    bioconda
pyyaml                    6.0             py310h5764c6d_5    conda-forge
qt                        5.15.4               hf11cfaa_0    conda-forge
qt-main                   5.15.4               ha5833f6_2    conda-forge
qt-webengine              5.15.4               hcbadb6c_3    conda-forge
quarto                    1.3.450              ha770c72_0    conda-forge
questionary               1.10.0             pyhd8ed1ab_1    conda-forge
r                         4.2             r42hd8ed1ab_1006    conda-forge
r-acepack                 1.4.1           r42h8da6f51_1007    conda-forge
r-ade4                    1.7_22            r42he1ae0d6_0    conda-forge
r-alakazam                1.0.2             r42h7525677_1    conda-forge
r-ape                     5.7_1             r42h358215d_0    conda-forge
r-askpass                 1.1               r42h06615bd_3    conda-forge
r-assertthat              0.2.1             r42hc72bb7e_3    conda-forge
r-backports               1.4.1             r42h06615bd_1    conda-forge
r-base                    4.2.1                h7880091_2    conda-forge
r-base64enc               0.1_3           r42h06615bd_1005    conda-forge
r-beeswarm                0.4.0             r42h06615bd_2    conda-forge
r-bh                      1.81.0_1          r42hc72bb7e_0    conda-forge
r-biocmanager             1.30.20           r42hc72bb7e_0    conda-forge
r-bit                     4.0.5             r42h06615bd_0    conda-forge
r-bit64                   4.0.5             r42h06615bd_1    conda-forge
r-bitops                  1.0_7             r42h06615bd_1    conda-forge
r-blob                    1.2.4             r42hc72bb7e_0    conda-forge
r-bookdown                0.33              r42hc72bb7e_0    conda-forge
r-boot                    1.3_28.1          r42hc72bb7e_0    conda-forge
r-brew                    1.0_8             r42hc72bb7e_1    conda-forge
r-brio                    1.1.3             r42h06615bd_1    conda-forge
r-broom                   1.0.4             r42hc72bb7e_0    conda-forge
r-bslib                   0.4.2             r42hc72bb7e_0    conda-forge
r-cachem                  1.0.7             r42h133d619_0    conda-forge
r-cairo                   1.6_0             r42h06615bd_1    conda-forge
r-callr                   3.7.3             r42hc72bb7e_0    conda-forge
r-cellranger              1.1.0           r42hc72bb7e_1005    conda-forge
r-checkmate               2.1.0             r42h06615bd_1    conda-forge
r-class                   7.3_21            r42h133d619_0    conda-forge
r-cli                     3.6.1             r42h38f115c_0    conda-forge
r-clipr                   0.8.0             r42hc72bb7e_1    conda-forge
r-clisymbols              1.2.0           r42hc72bb7e_1004    conda-forge
r-cluster                 2.1.4             r42h8da6f51_0    conda-forge
r-codetools               0.2_19            r42hc72bb7e_0    conda-forge
r-colorspace              2.1_0             r42h133d619_0    conda-forge
r-commonmark              1.9.0             r42h133d619_0    conda-forge
r-covr                    3.6.2             r42h38f115c_0    conda-forge
r-cpp11                   0.4.3             r42hc72bb7e_0    conda-forge
r-crayon                  1.5.2             r42hc72bb7e_1    conda-forge
r-credentials             1.3.2             r42hc72bb7e_1    conda-forge
r-crosstalk               1.2.0             r42hc72bb7e_1    conda-forge
r-crul                    1.3               r42h785f33e_1    conda-forge
r-curl                    4.3.3             r42h06615bd_1    conda-forge
r-data.table              1.14.8            r42h133d619_0    conda-forge
r-dbi                     1.1.3             r42hc72bb7e_1    conda-forge
r-dbplyr                  2.3.2             r42hc72bb7e_0    conda-forge
r-deldir                  1.0_6             r42h8da6f51_1    conda-forge
r-desc                    1.4.2             r42hc72bb7e_1    conda-forge
r-devtools                2.4.5             r42hc72bb7e_1    conda-forge
r-diffobj                 0.3.5             r42h06615bd_1    conda-forge
r-digest                  0.6.31            r42h38f115c_0    conda-forge
r-diptest                 0.76_0            r42h06615bd_1    conda-forge
r-distill                 1.5               r42hc72bb7e_1    conda-forge
r-doparallel              1.0.17            r42hc72bb7e_1    conda-forge
r-downlit                 0.4.2             r42hc72bb7e_1    conda-forge
r-dplyr                   1.1.1             r42h38f115c_0    conda-forge
r-dt                      0.27              r42hc72bb7e_0    conda-forge
r-dtplyr                  1.3.1             r42hc72bb7e_0    conda-forge
r-ellipsis                0.3.2             r42h06615bd_1    conda-forge
r-evaluate                0.20              r42hc72bb7e_0    conda-forge
r-fansi                   1.0.4             r42h133d619_0    conda-forge
r-farver                  2.1.1             r42h7525677_1    conda-forge
r-fastmap                 1.1.1             r42h38f115c_0    conda-forge
r-filelock                1.0.2           r42h133d619_1003    conda-forge
r-fontawesome             0.5.0             r42hc72bb7e_0    conda-forge
r-fontbitstreamvera       0.1.1           r42hc72bb7e_1004    conda-forge
r-fontliberation          0.1.0           r42hc72bb7e_1004    conda-forge
r-fontquiver              0.2.1           r42hc72bb7e_1004    conda-forge
r-forcats                 1.0.0             r42hc72bb7e_0    conda-forge
r-foreach                 1.5.2             r42hc72bb7e_1    conda-forge
r-foreign                 0.8_84            r42h133d619_0    conda-forge
r-formatr                 1.14              r42hc72bb7e_0    conda-forge
r-formula                 1.2_5             r42hc72bb7e_0    conda-forge
r-fs                      1.6.1             r42h38f115c_0    conda-forge
r-futile.logger           1.4.3           r42hc72bb7e_1004    conda-forge
r-futile.options          1.0.1           r42hc72bb7e_1003    conda-forge
r-gargle                  1.3.0             r42h785f33e_0    conda-forge
r-gdtools                 0.3.2             r42he0ce631_0    conda-forge
r-generics                0.1.3             r42hc72bb7e_1    conda-forge
r-gert                    1.5.0             r42h163148b_3    conda-forge
r-gfonts                  0.2.0             r42hc72bb7e_0    conda-forge
r-ggally                  2.1.2             r42hc72bb7e_1    conda-forge
r-ggbeeswarm              0.7.1             r42hc72bb7e_0    conda-forge
r-ggforce                 0.4.1             r42h7525677_1    conda-forge
r-ggiraph                 0.8.7             r42h38f115c_0    conda-forge
r-ggplot2                 3.4.1             r42hc72bb7e_0    conda-forge
r-ggpointdensity          0.1.0             r42h06615bd_2    conda-forge
r-ggrastr                 1.0.1             r42hc72bb7e_1    conda-forge
r-ggseqlogo               0.1             r42hc72bb7e_1004    conda-forge
r-gh                      1.4.0             r42hc72bb7e_0    conda-forge
r-git2r                   0.30.1            r42h96773ce_1    conda-forge
r-gitcreds                0.1.2             r42hc72bb7e_1    conda-forge
r-glue                    1.6.2             r42h06615bd_1    conda-forge
r-googledrive             2.1.0             r42hc72bb7e_0    conda-forge
r-googlesheets4           1.1.0             r42h785f33e_0    conda-forge
r-gridextra               2.3             r42hc72bb7e_1004    conda-forge
r-gtable                  0.3.3             r42hc72bb7e_0    conda-forge
r-gtools                  3.9.4             r42h06615bd_0    conda-forge
r-haven                   2.5.2             r42h38f115c_0    conda-forge
r-hdf5r                   1.3.8             r42haf92f5d_0    conda-forge
r-highr                   0.10              r42hc72bb7e_0    conda-forge
r-hmisc                   5.0_1             r42hac0b197_0    conda-forge
r-hms                     1.1.3             r42hc72bb7e_0    conda-forge
r-htmltable               2.4.1             r42hc72bb7e_1    conda-forge
r-htmltools               0.5.5             r42h38f115c_0    conda-forge
r-htmlwidgets             1.6.2             r42hc72bb7e_0    conda-forge
r-httpcode                0.3.0             r42ha770c72_2    conda-forge
r-httpuv                  1.6.9             r42h38f115c_0    conda-forge
r-httr                    1.4.5             r42hc72bb7e_0    conda-forge
r-httr2                   0.2.2             r42hc72bb7e_1    conda-forge
r-ids                     1.0.1             r42hc72bb7e_2    conda-forge
r-igraph                  1.3.5             r42hb34fc8a_0    conda-forge
r-ini                     0.3.1           r42hc72bb7e_1004    conda-forge
r-interp                  1.1_3             r42h7525677_1    conda-forge
r-isoband                 0.2.7             r42h38f115c_1    conda-forge
r-iterators               1.0.14            r42hc72bb7e_1    conda-forge
r-itertools               0.1_3           r42hc72bb7e_1004    conda-forge
r-jpeg                    0.1_10            r42h06615bd_0    conda-forge
r-jquerylib               0.1.4             r42hc72bb7e_1    conda-forge
r-jsonlite                1.8.4             r42h133d619_0    conda-forge
r-kableextra              1.3.4             r42hc72bb7e_1    conda-forge
r-kedd                    1.0.3           r42ha770c72_1005    conda-forge
r-kernsmooth              2.23_20           r42hd009a43_1    conda-forge
r-knitr                   1.42              r42hc72bb7e_1    conda-forge
r-labeling                0.4.2             r42hc72bb7e_2    conda-forge
r-lambda.r                1.2.4             r42hc72bb7e_2    conda-forge
r-later                   1.3.0             r42h7525677_1    conda-forge
r-lattice                 0.20_45           r42h06615bd_1    conda-forge
r-latticeextra            0.6_30            r42hc72bb7e_1    conda-forge
r-lazyeval                0.2.2             r42h06615bd_3    conda-forge
r-liblinear               2.10_22           r42h7525677_0    conda-forge
r-lifecycle               1.0.3             r42hc72bb7e_1    conda-forge
r-loomr                   0.2.0_beta        r42hdfd78af_4    bioconda
r-lubridate               1.9.2             r42h133d619_1    conda-forge
r-magick                  2.7.3             r42h7525677_1    conda-forge
r-magrittr                2.0.3             r42h06615bd_1    conda-forge
r-markdown                1.5               r42hc72bb7e_0    conda-forge
r-mass                    7.3_58.3          r42h133d619_0    conda-forge
r-matrix                  1.5_3             r42h5f7b363_0    conda-forge
r-matrixstats             0.63.0            r42h06615bd_0    conda-forge
r-memoise                 2.0.1             r42hc72bb7e_1    conda-forge
r-mgcv                    1.8_42            r42he1ae0d6_0    conda-forge
r-mime                    0.12              r42h06615bd_1    conda-forge
r-miniui                  0.1.1.1         r42hc72bb7e_1003    conda-forge
r-modelr                  0.1.11            r42hc72bb7e_0    conda-forge
r-munsell                 0.5.0           r42hc72bb7e_1005    conda-forge
r-nlme                    3.1_162           r42hac0b197_0    conda-forge
r-nnet                    7.3_18            r42h06615bd_1    conda-forge
r-openssl                 2.0.5             r42hb1dc35e_0    conda-forge
r-patchwork               1.1.2             r42hc72bb7e_1    conda-forge
r-pillar                  1.9.0             r42hc72bb7e_0    conda-forge
r-pixmap                  0.4_12            r42hc72bb7e_1    conda-forge
r-pkgbuild                1.4.0             r42hc72bb7e_0    conda-forge
r-pkgconfig               2.0.3             r42hc72bb7e_2    conda-forge
r-pkgdown                 2.0.7             r42hc72bb7e_0    conda-forge
r-pkgload                 1.3.2             r42hc72bb7e_0    conda-forge
r-plogr                   0.2.0           r42hc72bb7e_1004    conda-forge
r-plyr                    1.8.8             r42h7525677_0    conda-forge
r-png                     0.1_8             r42h10cf519_0    conda-forge
r-polyclip                1.10_4            r42h7525677_0    conda-forge
r-praise                  1.0.0           r42hc72bb7e_1006    conda-forge
r-prettyunits             1.1.1             r42hc72bb7e_2    conda-forge
r-processx                3.8.0             r42h06615bd_0    conda-forge
r-profvis                 0.3.7             r42h06615bd_1    conda-forge
r-progress                1.2.2             r42hc72bb7e_3    conda-forge
r-promises                1.2.0.1           r42h7525677_1    conda-forge
r-ps                      1.7.3             r42h133d619_0    conda-forge
r-purrr                   1.0.1             r42h133d619_0    conda-forge
r-purrrlyr                0.0.8             r42h7525677_1    conda-forge
r-r.methodss3             1.8.2             r42hc72bb7e_1    conda-forge
r-r.oo                    1.25.0            r42hc72bb7e_1    conda-forge
r-r.utils                 2.12.2            r42hc72bb7e_0    conda-forge
r-r6                      2.5.1             r42hc72bb7e_1    conda-forge
r-ragg                    1.2.4             r42hc1f6985_0    conda-forge
r-rappdirs                0.3.3             r42h06615bd_1    conda-forge
r-rcmdcheck               1.4.0             r42h785f33e_1    conda-forge
r-rcolorbrewer            1.1_3             r42h785f33e_1    conda-forge
r-rcpp                    1.0.10            r42h38f115c_0    conda-forge
r-rcppeigen               0.3.3.9.3         r42h9f5de39_0    conda-forge
r-rcurl                   1.98_1.9          r42h06615bd_1    conda-forge
r-readr                   2.1.4             r42h38f115c_0    conda-forge
r-readxl                  1.4.2             r42h81ef4d7_0    conda-forge
r-recommended             4.2             r42hd8ed1ab_1005    conda-forge
r-rematch                 1.0.1           r42hc72bb7e_1005    conda-forge
r-rematch2                2.1.2             r42hc72bb7e_2    conda-forge
r-remotes                 2.4.2             r42hc72bb7e_1    conda-forge
r-reprex                  2.0.2             r42hc72bb7e_1    conda-forge
r-reshape                 0.8.9             r42hc72bb7e_1    conda-forge
r-reshape2                1.4.4             r42h7525677_2    conda-forge
r-restfulr                0.0.15            r42h73dbb54_1    bioconda
r-rex                     1.2.1             r42hc72bb7e_1    conda-forge
r-rjson                   0.2.21            r42h7525677_2    conda-forge
r-rlang                   1.1.0             r42h38f115c_0    conda-forge
r-rmarkdown               2.24              r42hc72bb7e_0    conda-forge
r-roxygen2                7.2.3             r42h38f115c_0    conda-forge
r-rpart                   4.1.19            r42h06615bd_0    conda-forge
r-rprojroot               2.0.3             r42hc72bb7e_1    conda-forge
r-rsqlite                 2.3.0             r42h38f115c_0    conda-forge
r-rstudioapi              0.14              r42hc72bb7e_1    conda-forge
r-rversions               2.1.2             r42hc72bb7e_1    conda-forge
r-rvest                   1.0.3             r42hc72bb7e_1    conda-forge
r-sass                    0.4.5             r42h38f115c_0    conda-forge
r-scales                  1.2.1             r42hc72bb7e_1    conda-forge
r-sdmtools                1.1_221.2         r42h06615bd_2    conda-forge
r-segmented               1.6_3             r42hc72bb7e_0    conda-forge
r-selectr                 0.4_2             r42hc72bb7e_2    conda-forge
r-seqinr                  4.2_23            r42h06615bd_0    conda-forge
r-sessioninfo             1.2.2             r42hc72bb7e_1    conda-forge
r-shazam                  1.0.2             r42hc72bb7e_1    conda-forge
r-shiny                   1.7.4             r42h785f33e_0    conda-forge
r-snow                    0.4_4             r42hc72bb7e_1    conda-forge
r-sourcetools             0.1.7_1           r42h38f115c_0    conda-forge
r-sp                      1.6_0             r42h133d619_0    conda-forge
r-spatial                 7.3_16            r42h133d619_0    conda-forge
r-stringdist              0.9.10            r42h06615bd_0    conda-forge
r-stringi                 1.7.12            r42h1ae9187_0    conda-forge
r-stringr                 1.5.0             r42h785f33e_0    conda-forge
r-survival                3.5_5             r42h133d619_0    conda-forge
r-svglite                 2.1.1             r42he8f5e61_0    conda-forge
r-sys                     3.4.1             r42h06615bd_0    conda-forge
r-systemfonts             1.0.4             r42h0ff29ef_1    conda-forge
r-testthat                3.1.7             r42h38f115c_0    conda-forge
r-textshaping             0.3.6             r42hbb20487_4    conda-forge
r-tibble                  3.2.1             r42h133d619_1    conda-forge
r-tidyr                   1.3.0             r42h38f115c_0    conda-forge
r-tidyselect              1.2.0             r42hc72bb7e_0    conda-forge
r-tidyverse               1.3.2             r42hc72bb7e_1    conda-forge
r-tigger                  1.0.0             r42hc72bb7e_2    conda-forge
r-timechange              0.2.0             r42h38f115c_0    conda-forge
r-tinytex                 0.44              r42hc72bb7e_0    conda-forge
r-triebeard               0.4.1             r42h38f115c_0    conda-forge
r-tweenr                  2.0.2             r42h7525677_1    conda-forge
r-tzdb                    0.3.0             r42h7525677_1    conda-forge
r-urlchecker              1.0.1             r42hc72bb7e_1    conda-forge
r-urltools                1.7.3             r42h7525677_3    conda-forge
r-usethis                 2.1.6             r42hc72bb7e_1    conda-forge
r-utf8                    1.2.3             r42h133d619_0    conda-forge
r-uuid                    1.1_0             r42h06615bd_1    conda-forge
r-vctrs                   0.6.1             r42h38f115c_0    conda-forge
r-vipor                   0.4.5           r42hc72bb7e_1004    conda-forge
r-viridis                 0.6.2             r42hc72bb7e_1    conda-forge
r-viridislite             0.4.1             r42hc72bb7e_1    conda-forge
r-vroom                   1.6.1             r42h38f115c_0    conda-forge
r-waldo                   0.4.0             r42hc72bb7e_1    conda-forge
r-webshot                 0.5.4             r42hc72bb7e_1    conda-forge
r-whisker                 0.4.1             r42hc72bb7e_0    conda-forge
r-withr                   2.5.0             r42hc72bb7e_1    conda-forge
r-xfun                    0.38              r42h38f115c_0    conda-forge
r-xml                     3.99_0.11         r42h2b86b34_2    conda-forge
r-xml2                    1.3.3             r42h044e5c7_2    conda-forge
r-xopen                   1.0.0           r42hc72bb7e_1004    conda-forge
r-xtable                  1.8_4             r42hc72bb7e_4    conda-forge
r-yaml                    2.3.7             r42h133d619_0    conda-forge
r-zeallot                 0.1.0           r42hc72bb7e_1004    conda-forge
r-zip                     2.2.2             r42h06615bd_0    conda-forge
readline                  8.2                  h8228510_1    conda-forge
refgenconf                0.12.2             pyhdfd78af_0    bioconda
refgenie                  0.12.1             pyhdfd78af_0    bioconda
regex                     2023.3.23       py310h1fa729e_0    conda-forge
repoze.lru                0.7                        py_0    conda-forge
reproc                    14.2.4               h0b41bf4_0    conda-forge
reproc-cpp                14.2.4               hcb278e6_0    conda-forge
requests                  2.28.2             pyhd8ed1ab_0    conda-forge
requests-cache            1.0.1              pyhd8ed1ab_0    conda-forge
rich                      13.3.2             pyhd8ed1ab_0    conda-forge
rich-click                1.6.1              pyhd8ed1ab_0    conda-forge
routes                    2.5.1              pyhd8ed1ab_0    conda-forge
ruamel.yaml               0.17.21         py310h1fa729e_3    conda-forge
ruamel.yaml.clib          0.2.7           py310h1fa729e_1    conda-forge
rust                      1.67.1               hefb9f0a_0    conda-forge
rust-std-x86_64-unknown-linux-gnu 1.67.1               hc1431ca_0    conda-forge
samtools                  1.16.1               h6899075_1    bioconda
scipy                     1.10.1          py310h8deb116_0    conda-forge
sed                       4.8                  he412f7d_0    conda-forge
seqtk                     1.3                  h7132678_4    bioconda
setuptools                67.6.0             pyhd8ed1ab_0    conda-forge
simplejson                3.18.4          py310h1fa729e_0    conda-forge
sip                       6.6.2           py310hd8f1fbe_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
smmap                     3.0.5              pyh44b312d_0    conda-forge
sortedcontainers          2.4.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.4.1                    pypi_0    pypi
spectra                   0.0.11                     py_1    conda-forge
sqlite                    3.40.0               h4ff8645_0    conda-forge
sra-tools                 3.0.3                h87f3376_0    bioconda
starship                  1.13.1               hbd0da30_0    conda-forge
sysroot_linux-64          2.12                he073ed8_15    conda-forge
tabulate                  0.9.0              pyhd8ed1ab_1    conda-forge
tbl2asn                   25.7                 h9ee0642_1    bioconda
text-unidecode            1.3                        py_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
tktable                   2.10                 hb7b940f_3    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
toolz                     0.12.0             pyhd8ed1ab_0    conda-forge
tornado                   6.2             py310h5764c6d_1    conda-forge
tqdm                      4.65.0             pyhd8ed1ab_1    conda-forge
typing                    3.10.0.0           pyhd8ed1ab_0    conda-forge
typing-extensions         4.5.0                hd8ed1ab_0    conda-forge
typing_extensions         4.5.0              pyha770c72_0    conda-forge
tzdata                    2023b                h71feb2d_0    conda-forge
ubiquerg                  0.6.2              pyhd8ed1ab_0    conda-forge
ujson                     5.7.0           py310heca2aa9_0    conda-forge
ukkonen                   1.0.1           py310hbf28c38_3    conda-forge
unicodedata2              15.0.0          py310h5764c6d_0    conda-forge
unidecode                 1.3.6              pyhd8ed1ab_0    conda-forge
url-normalize             1.4.3              pyhd8ed1ab_0    conda-forge
urllib3                   1.26.15            pyhd8ed1ab_0    conda-forge
veracitools               0.1.3                      py_0    conda-forge
virtualenv                20.21.0            pyhd8ed1ab_0    conda-forge
vsearch                   2.22.1               hf1761c0_0    bioconda
wcwidth                   0.2.6              pyhd8ed1ab_0    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wget                      1.20.3               ha56f1ee_1    conda-forge
wheel                     0.40.0             pyhd8ed1ab_0    conda-forge
whoosh                    2.7.4           py310hff52083_7    conda-forge
xcb-util                  0.4.0                h516909a_0    conda-forge
xcb-util-image            0.4.0                h166bdaf_0    conda-forge
xcb-util-keysyms          0.4.0                h516909a_0    conda-forge
xcb-util-renderutil       0.3.9                h166bdaf_0    conda-forge
xcb-util-wm               0.4.1                h516909a_0    conda-forge
xmltodict                 0.13.0             pyhd8ed1ab_0    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.0.10               h7f98852_0    conda-forge
xorg-libsm                1.2.3             hd9c2040_1000    conda-forge
xorg-libx11               1.8.4                h0b41bf4_0    conda-forge
xorg-libxau               1.0.9                h7f98852_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h0b41bf4_2    conda-forge
xorg-libxrender           0.9.10            h7f98852_1003    conda-forge
xorg-libxt                1.2.1                h7f98852_2    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h0b41bf4_1003    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xyzservices               2023.5.0                 pypi_0    pypi
xz                        5.2.6                h166bdaf_0    conda-forge
yacman                    0.9.0              pyhd8ed1ab_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
yaml-cpp                  0.7.0                h27087fc_2    conda-forge
yq                        3.1.1              pyhd8ed1ab_0    conda-forge
zipp                      3.15.0             pyhd8ed1ab_0    conda-forge
zipstream-new             1.1.8              pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               h166bdaf_4    conda-forge
zsh                       5.8                  h3d38e88_1    conda-forge
zstandard                 0.19.0          py310hdeb6495_1    conda-forge
zstd                      1.5.2                h3eb15da_6    conda-forge

Environment info

❯ conda info

     active environment : base
    active env location : /users/ido.tamir/.conda/envs/mamba/envs/bioinfo
            shell level : 2
       user config file : /users/ido.tamir/.condarc
 populated config files : /users/ido.tamir/.condarc
          conda version : 23.7.2
    conda-build version : not installed
         python version : 3.10.8.final.0
       virtual packages : __archspec=1=x86_64
                          __glibc=2.17=0
                          __linux=3.10.0=0
                          __unix=0=0
       base environment : /users/ido.tamir/.conda/envs/mamba/envs/bioinfo  (writable)
      conda av data dir : /users/ido.tamir/.conda/envs/mamba/envs/bioinfo/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /users/ido.tamir/.conda/envs/mamba/envs/bioinfo/pkgs
                          /users/ido.tamir/.conda/pkgs
       envs directories : /users/ido.tamir/.conda/envs/mamba/envs/bioinfo/envs
                          /users/ido.tamir/.conda/envs
               platform : linux-64
             user-agent : conda/23.7.2 requests/2.28.2 CPython/3.10.8 Linux/3.10.0-1160.80.1.el7.x86_64 centos/7.9.2009 glibc/2.17
                UID:GID : 50039:2057
             netrc file : None
           offline mode : False
mfisher87 commented 1 year ago

Thanks for reporting this!

I was not able to reproduce on my end. Can you please activate a conda environment with quarto installed and report the result of env | grep QUARTO? I suspect this envvar is not be set in your conda environment and is therefore being calculated by the run script.

On my machine:

$ env | grep QUARTO
...
QUARTO_DENO=/home/me/.local/share/miniconda3/envs/quarto-test-29/bin/deno
...

On your machine, these vars should be set at /users/ido.tamir/.conda/envs/mamba/envs/bioinfo/etc/conda/activate.d/quarto.sh

mfisher87 commented 1 year ago

I think I see a potential cause. /users/ido.tamir/.conda/envs/mamba/envs/bioinfo This doesn't look right to me. mamba should be installed in your base conda environment, not in its own dedicated environment.

The mamba install docs provide good instructions. However, they strongly recommend against installing mamba into a pre-existing conda install, I believe because it's easy to get in to this situation. Especially important note from that page: Installing mamba into any other environment than base is not supported.

Please let us know if we can close this issue or if you continue to experience issues after fixing the mamba installation.

idot commented 1 year ago

Dear Matt, thank you very much for your help. You can close this issue.

best, ido

mfisher87 commented 1 year ago

My pleasure, Ido, thanks for taking the time to report!