Cannot get biobakery_workflows vis to run

Infrastructure and utilities bioBakery workflows
11

BIG NEWS!

I finally managed to get biobakery_workflows vis to run!

The solution that worked for me:

  1. Create conda env, but not installing biobakery_workflows
    mamba create -n biobakery_test python=3.7 pip zip gxx_linux-64 pandoc R
    (If you don’t know mamba, it is a drop-in replacement of conda that is much faster)

  2. Go inside the environment:
    conda activate biobakery_test

  3. Install biobakery_workflows and dependencies with pip:
    pip install numpy matplotlib humann scipy biobakery_workflows
    Warning: it is NOT recommended to mix pip and conda installs. However, installing packages with pip is OK as long as you do not install anything afterwards with conda (i.e: conda first, pip then), as per conda documentation.

  4. As observed previously (see first post), there is a path problem with images included for biobakery_workflow vis. Creating a symlink did the trick for me:
    ln -s /home/theoscilicium/miniconda3/envs/biobakery/images /home/theoscilicium/miniconda3/envs/biobakery/lib/python3.7/site-packages/images

  5. This is probably config-dependent and may vary in your setup, and from what I read cannot be easily deported to a conda env, but at this step I had to install additional packages for latex:
    sudo apt-get install texlive-latex-extra

  6. Run biobakery workflows!
    biobakery_workflows vis --input run_test/biobakery_results/ --output run_test/vis/ --project-name TEST

  7. Exit conda env:
    conda deactivate

Hope this can help other people! Included bellow are further information about the setup.

Best,
Theo

Output of conda list

packages in environment at /home/theoscilicium/miniconda3/envs/biobakery_test:

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
_r-mutex 1.0.1 anacondar_1 conda-forge
anadama2 0.10.0 pypi_0 pypi
binutils_impl_linux-64 2.39 h6ceecb4_0 conda-forge
binutils_linux-64 2.39 h5fc0e48_11 conda-forge
biobakery-workflows 3.1 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 2022.9.24 ha878542_0 conda-forge
cairo 1.16.0 ha61ee94_1014 conda-forge
cloudpickle 2.2.0 pypi_0 pypi
curl 7.86.0 h2283fc2_1 conda-forge
cycler 0.11.0 pypi_0 pypi
expat 2.5.0 h27087fc_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 2.14.1 hc2a2eb6_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.38.0 pypi_0 pypi
freetype 2.12.1 hca18f0e_0 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
gcc_impl_linux-64 12.2.0 hcc96c02_19 conda-forge
gcc_linux-64 12.2.0 h4798a0e_11 conda-forge
gettext 0.21.1 h27087fc_0 conda-forge
gfortran_impl_linux-64 12.2.0 h55be85b_19 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
gsl 2.7 he838d99_0 conda-forge
gxx_impl_linux-64 12.2.0 hcc96c02_19 conda-forge
gxx_linux-64 12.2.0 hb41e900_11 conda-forge
harfbuzz 5.3.0 h418a68e_0 conda-forge
humann 3.6 pypi_0 pypi
icu 70.1 h27087fc_0 conda-forge
importlib-metadata 5.0.0 pypi_0 pypi
jpeg 9e h166bdaf_2 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 pypi_0 pypi
krb5 1.19.3 h08a2579_0 conda-forge
ld_impl_linux-64 2.39 hc81fddc_0 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
leveldb 0.201 pypi_0 pypi
libblas 3.9.0 16_linux64_openblas conda-forge
libcblas 3.9.0 16_linux64_openblas conda-forge
libcurl 7.86.0 h2283fc2_1 conda-forge
libdeflate 1.14 h166bdaf_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-devel_linux-64 12.2.0 h3b97bd3_19 conda-forge
libgcc-ng 12.2.0 h65d4601_19 conda-forge
libgfortran-ng 12.2.0 h69a702a_19 conda-forge
libgfortran5 12.2.0 h337968e_19 conda-forge
libglib 2.74.1 h606061b_1 conda-forge
libgomp 12.2.0 h65d4601_19 conda-forge
libiconv 1.17 h166bdaf_0 conda-forge
liblapack 3.9.0 16_linux64_openblas conda-forge
libnghttp2 1.47.0 hff17c54_1 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge
libpng 1.6.38 h753d276_0 conda-forge
libsanitizer 12.2.0 h46fd767_19 conda-forge
libsqlite 3.39.4 h753d276_0 conda-forge
libssh2 1.10.0 hf14f497_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 h55922b4_4 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libwebp-base 1.2.4 h166bdaf_0 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxml2 2.10.3 h7463322_0 conda-forge
libzlib 1.2.13 h166bdaf_4 conda-forge
make 4.3 hd18ef5c_1 conda-forge
markdown 3.4.1 pypi_0 pypi
matplotlib 3.5.3 pypi_0 pypi
ncurses 6.3 h27087fc_1 conda-forge
networkx 2.6.3 pypi_0 pypi
numpy 1.21.6 pypi_0 pypi
openssl 3.0.7 h166bdaf_0 conda-forge
packaging 21.3 pypi_0 pypi
pandoc 2.19.2 h32600fe_1 conda-forge
pango 1.50.11 h382ae3d_0 conda-forge
pcre2 10.40 hc3806b6_0 conda-forge
pillow 9.3.0 pypi_0 pypi
pip 22.3.1 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pweave 0.25 pypi_0 pypi
pyparsing 3.0.9 pypi_0 pypi
python 3.7.12 hf930737_100_cpython conda-forge
python-dateutil 2.8.2 pypi_0 pypi
r 4.2 r42hd8ed1ab_1006 conda-forge
r-base 4.2.2 hb87df5d_1 conda-forge
r-boot 1.3_28 r42hc72bb7e_1 conda-forge
r-class 7.3_20 r42h06615bd_1 conda-forge
r-cluster 2.1.4 r42h8da6f51_0 conda-forge
r-codetools 0.2_18 r42hc72bb7e_1 conda-forge
r-foreign 0.8_83 r42h06615bd_1 conda-forge
r-kernsmooth 2.23_20 r42hd009a43_1 conda-forge
r-lattice 0.20_45 r42h06615bd_1 conda-forge
r-mass 7.3_58.1 r42h06615bd_1 conda-forge
r-matrix 1.5_1 r42h5f7b363_0 conda-forge
r-mgcv 1.8_41 r42h5f7b363_0 conda-forge
r-nlme 3.1_160 r42h8da6f51_0 conda-forge
r-nnet 7.3_18 r42h06615bd_1 conda-forge
r-recommended 4.2 r42hd8ed1ab_1005 conda-forge
r-rpart 4.1.19 r42h06615bd_0 conda-forge
r-spatial 7.3_15 r42h06615bd_1 conda-forge
r-survival 3.4_0 r42h06615bd_1 conda-forge
readline 8.1.2 h0f457ee_0 conda-forge
scipy 1.7.3 pypi_0 pypi
sed 4.8 he412f7d_0 conda-forge
setuptools 65.5.1 pyhd8ed1ab_0 conda-forge
six 1.16.0 pypi_0 pypi
sqlite 3.39.4 h4ff8645_0 conda-forge
sysroot_linux-64 2.12 he073ed8_15 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tktable 2.10 hb7b940f_3 conda-forge
typing-extensions 4.4.0 pypi_0 pypi
wheel 0.38.2 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 1.7.2 h7f98852_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 h7f98852_1 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 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
zip 3.0 h7f98852_1 conda-forge
zipp 3.10.0 pypi_0 pypi
zlib 1.2.13 h166bdaf_4 conda-forge
zstd 1.5.2 h6239696_4 conda-forge

Output of pip freeze

anadama2==0.10.0
biobakery-workflows==3.1
cloudpickle==2.2.0
cycler==0.11.0
fonttools==4.38.0
humann==3.6
importlib-metadata==5.0.0
kiwisolver==1.4.4
leveldb==0.201
Markdown==3.4.1
matplotlib==3.5.3
networkx==2.6.3
numpy==1.21.6
packaging==21.3
Pillow==9.3.0
Pweave==0.25
pyparsing==3.0.9
python-dateutil==2.8.2
scipy==1.7.3
six==1.16.0
typing_extensions==4.4.0
zipp==3.10.0

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