Biomni
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snap-stanford
No module named when running agent.go()
Hi team,
I have setup full E1 with
bash setup.sh
but when running agent.go() from A1 with prompt i got the issue. No module named like rdkit, PyPDF2,...
How i can resolve this issues. Thanks
# Visualize the molecule
Draw.MolToImage(molecule)
</execute>
================================== Ai Message ==================================
<observation>Error: No module named 'rdkit'</observation>
================================== Ai Message ==================================
It seems the `rdkit` package is not available in the current environment, which is essential for converting SMILES strings to molecular structures. To proceed, we will need to ensure that the necessary packages are available. Since I'm unable to directly install packages, I'll adjust the plan to focus on other aspects that can be executed here.
Hi @tien-genetica,
maybe try to make sure that all the packages in the bio_env.yaml are all installed properly.
run the when u are inside the Biomni_env directory
bash setup.sh
The script will ask u to ccontinue or not because u have the environment already exist so just say: yes with (y)
see the installations of the tools maybe some are missing.
another way to check is here is the full list
conda list -n biomni_e1
"# 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
absl-py 2.3.1 pypi_0 pypi
aiobotocore 2.23.1 pypi_0 pypi
aiofiles 24.1.0 pypi_0 pypi
aiohappyeyeballs 2.6.1 pypi_0 pypi
aiohttp 3.12.14 pypi_0 pypi
aioitertools 0.12.0 pypi_0 pypi
aiosignal 1.4.0 pypi_0 pypi
alabaster 1.0.0 pypi_0 pypi
alsa-lib 1.2.14 hb9d3cd8_0 conda-forge
altair 5.5.0 pyhd8ed1ab_1 conda-forge
anndata 0.12.0 pypi_0 pypi
annotated-types 0.7.0 pypi_0 pypi
annoy 1.17.3 pypi_0 pypi
anthropic 0.57.1 pypi_0 pypi
anyio 4.9.0 pyh29332c3_0 conda-forge
appdirs 1.4.4 pypi_0 pypi
arboreto 0.1.6 pypi_0 pypi
argon2-cffi 25.1.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py311h9ecbd09_5 conda-forge
array-api-compat 1.12.0 pypi_0 pypi
arrow 1.3.0 pyhd8ed1ab_1 conda-forge
arviz 0.22.0 pypi_0 pypi
arxiv 2.2.0 pypi_0 pypi
asciitree 0.3.3 pypi_0 pypi
asttokens 3.0.0 pyhd8ed1ab_1 conda-forge
async-lru 2.0.5 pyh29332c3_0 conda-forge
attrs 25.3.0 pyh71513ae_0 conda-forge
autograd 1.8.0 pypi_0 pypi
autograd-gamma 0.5.0 pypi_0 pypi
aws-c-auth 0.9.0 h92a005d_16 conda-forge
aws-c-cal 0.9.2 he7b75e1_1 conda-forge
aws-c-common 0.12.4 hb03c661_0 conda-forge
aws-c-compression 0.3.1 h92c474e_6 conda-forge
aws-c-event-stream 0.5.5 h0c2b49e_1 conda-forge
aws-c-http 0.10.2 hee85082_3 conda-forge
aws-c-io 0.21.0 h1d8da38_1 conda-forge
aws-c-mqtt 0.13.1 h46c1de9_4 conda-forge
aws-c-s3 0.8.4 h9cdc349_0 conda-forge
aws-c-sdkutils 0.2.4 h92c474e_1 conda-forge
aws-checksums 0.2.7 h92c474e_2 conda-forge
aws-crt-cpp 0.33.0 he2a3bdb_1 conda-forge
aws-sdk-cpp 1.11.510 h455e09b_15 conda-forge
azure-core-cpp 1.15.0 h5cfcd09_0 conda-forge
azure-identity-cpp 1.11.0 hb5324b0_1 conda-forge
azure-storage-blobs-cpp 12.13.0 hf182047_2 conda-forge
azure-storage-common-cpp 12.10.0 h40e822a_1 conda-forge
azure-storage-files-datalake-cpp 12.12.0 h141ff2a_2 conda-forge
babel 2.17.0 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.13.4 pyha770c72_0 conda-forge
bedtools 2.31.1 h13024bc_3 bioconda
bibtexparser 1.4.3 pypi_0 pypi
binutils_impl_linux-64 2.44 h4bf12b8_1 conda-forge
biom-format 2.1.16 pypi_0 pypi
biopandas 0.5.1 pypi_0 pypi
biopython 1.85 py311h9ecbd09_1 conda-forge
biotite 1.4.0 pypi_0 pypi
biotraj 1.2.2 pypi_0 pypi
blast 2.16.0 h66d330f_5 bioconda
bleach 6.2.0 pyh29332c3_4 conda-forge
bleach-with-css 6.2.0 h82add2a_4 conda-forge
blinker 1.9.0 pyhff2d567_0 conda-forge
blosc2 3.6.1 pypi_0 pypi
bokeh 3.7.3 pyhd8ed1ab_0 conda-forge
boltons 25.0.0 pypi_0 pypi
boto3 1.39.9 pypi_0 pypi
botocore 1.38.46 pypi_0 pypi
bowtie2 2.5.4 he96a11b_6 bioconda
brotli 1.1.0 pypi_0 pypi
brotli-bin 1.1.0 hb9d3cd8_3 conda-forge
brotli-python 1.1.0 py311hfdbb021_3 conda-forge
bwa 0.7.19 h577a1d6_1 bioconda
bwidget 1.10.1 ha770c72_1 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.5 hb9d3cd8_0 conda-forge
ca-certificates 2025.7.14 hbd8a1cb_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachetools 5.5.2 pypi_0 pypi
cairo 1.18.4 h3394656_0 conda-forge
cellpose 4.0.6 pypi_0 pypi
cellxgene-census 1.17.0 pypi_0 pypi
certifi 2025.7.14 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py311hf29c0ef_0 conda-forge
cftime 1.6.4.post1 pypi_0 pypi
charset-normalizer 3.4.2 pyhd8ed1ab_0 conda-forge
chex 0.1.89 pypi_0 pypi
click 8.2.1 pyh707e725_0 conda-forge
clikit 0.6.2 pypi_0 pypi
cloudpickle 3.1.1 pypi_0 pypi
cobra 0.29.1 pypi_0 pypi
coloredlogs 15.0.1 pypi_0 pypi
comm 0.2.2 pyhd8ed1ab_1 conda-forge
community 1.0.0b1 pypi_0 pypi
contourpy 1.3.2 py311hd18a35c_0 conda-forge
cooler 0.10.4 pypi_0 pypi
crashtest 0.3.1 pypi_0 pypi
crc32c 2.7.1 pypi_0 pypi
cryosparc-tools 4.7.1 pypi_0 pypi
ctxcore 0.2.0 pypi_0 pypi
curl 8.14.1 h332b0f4_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_1 conda-forge
cython 0.29.37 pypi_0 pypi
cytoolz 1.0.1 pypi_0 pypi
cyvcf2 0.31.1 pypi_0 pypi
dask 2025.7.0 pypi_0 pypi
dataclasses 0.6 pypi_0 pypi
dataclasses-json 0.6.7 pypi_0 pypi
debugpy 1.8.15 pypi_0 pypi
decorator 5.2.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
demes 0.2.3 pypi_0 pypi
depinfo 2.2.0 pypi_0 pypi
deprecated 1.2.18 pypi_0 pypi
deprecation 2.1.0 pypi_0 pypi
diamond 2.1.12 h13889ed_3 bioconda
dill 0.4.0 pypi_0 pypi
diskcache 5.6.3 pypi_0 pypi
distributed 2025.7.0 pypi_0 pypi
distro 1.9.0 pypi_0 pypi
docrep 0.3.2 pypi_0 pypi
docutils 0.21.2 pypi_0 pypi
domdf-python-tools 3.10.0 pypi_0 pypi
donfig 0.8.1.post1 pypi_0 pypi
drmaa 0.7.9 pypi_0 pypi
entrez-direct 22.4 he881be0_0 bioconda
enum-tools 0.13.0 pypi_0 pypi
et-xmlfile 2.0.0 pypi_0 pypi
etils 1.13.0 pypi_0 pypi
exceptiongroup 1.3.0 pyhd8ed1ab_0 conda-forge
executing 2.2.0 pyhd8ed1ab_0 conda-forge
faiss-cpu 1.11.0.post1 pypi_0 pypi
fake-useragent 2.2.0 pypi_0 pypi
fanc 0.9.28 pypi_0 pypi
fastapi 0.116.1 pypi_0 pypi
fastprogress 1.0.3 pypi_0 pypi
fastqc 0.12.1 hdfd78af_0 bioconda
fastremap 1.17.1 pypi_0 pypi
fcsparser 0.2.4 pypi_0 pypi
feedparser 6.0.11 pypi_0 pypi
ffmpy 0.6.0 pypi_0 pypi
filelock 3.18.0 pypi_0 pypi
filetype 1.2.0 pypi_0 pypi
fill-voids 2.1.0 pypi_0 pypi
flask 3.1.1 pypi_0 pypi
flax 0.10.7 pypi_0 pypi
flowcytometrytools 0.5.1 pypi_0 pypi
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 h77eed37_3 conda-forge
fontconfig 2.15.0 h7e30c49_1 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.59.0 py311h3778330_0 conda-forge
formulaic 1.2.0 pypi_0 pypi
fqdn 1.5.1 pyhd8ed1ab_1 conda-forge
free-proxy 1.1.3 pypi_0 pypi
freetype 2.13.3 ha770c72_1 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
frozendict 2.4.6 pypi_0 pypi
frozenlist 1.7.0 pypi_0 pypi
fsspec 2025.7.0 pypi_0 pypi
future 1.0.0 pypi_0 pypi
fuzzywuzzy 0.18.0 pypi_0 pypi
gawk 5.3.1 hcd3d067_0 conda-forge
gcc_impl_linux-64 15.1.0 h4393ad2_3 conda-forge
genomic-regions 0.0.10 pypi_0 pypi
gflags 2.2.2 h5888daf_1005 conda-forge
gfortran_impl_linux-64 15.1.0 h3b9cdf2_3 conda-forge
gget 0.29.2 pypi_0 pypi
giflib 5.2.2 hd590300_0 conda-forge
gitdb 4.0.12 pyhd8ed1ab_0 conda-forge
gitpython 3.1.44 pyhff2d567_0 conda-forge
glog 0.7.1 hbabe93e_0 conda-forge
gmp 6.3.0 hac33072_2 conda-forge
google-ai-generativelanguage 0.6.18 pypi_0 pypi
google-api-core 2.25.1 pypi_0 pypi
google-auth 2.40.3 pypi_0 pypi
googleapis-common-protos 1.70.0 pypi_0 pypi
googlesearch-python 1.3.0 pypi_0 pypi
gradio 5.38.0 pypi_0 pypi
gradio-client 1.11.0 pypi_0 pypi
graphite2 1.3.14 h5888daf_0 conda-forge
greenlet 3.2.3 pypi_0 pypi
gridmap 0.15.0 pypi_0 pypi
groovy 0.1.2 pypi_0 pypi
grpcio 1.73.1 pypi_0 pypi
grpcio-status 1.73.1 pypi_0 pypi
gseapy 1.1.9 py311h5e00ca1_0 bioconda
gsl 2.7 he838d99_0 conda-forge
gxx_impl_linux-64 15.1.0 h6a1bac1_3 conda-forge
h11 0.16.0 pyhd8ed1ab_0 conda-forge
h2 4.2.0 pyhd8ed1ab_0 conda-forge
h5netcdf 1.6.3 pypi_0 pypi
h5py 3.14.0 pypi_0 pypi
harfbuzz 11.2.1 h3beb420_0 conda-forge
harmony-pytorch 0.1.8 pypi_0 pypi
hf-xet 1.1.5 pypi_0 pypi
hmmlearn 0.3.3 pypi_0 pypi
hpack 4.1.0 pyhd8ed1ab_0 conda-forge
htslib 1.22 h566b1c6_0 bioconda
httpcore 1.0.9 pyh29332c3_0 conda-forge
httpstan 4.13.0 pypi_0 pypi
httpx 0.28.1 pyhd8ed1ab_0 conda-forge
httpx-sse 0.4.1 pypi_0 pypi
huggingface-hub 0.33.4 pypi_0 pypi
humanfriendly 10.0 pypi_0 pypi
humanize 4.12.3 pypi_0 pypi
hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge
icu 75.1 he02047a_0 conda-forge
idna 3.10 pyhd8ed1ab_1 conda-forge
igraph 0.11.9 pypi_0 pypi
imagecodecs 2025.3.30 pypi_0 pypi
imageio 2.37.0 pypi_0 pypi
imagesize 1.4.1 pypi_0 pypi
importlib-metadata 8.7.0 pyhe01879c_1 conda-forge
importlib_resources 6.5.2 pyhd8ed1ab_0 conda-forge
infernal 1.1.5 pl5321h7b50bb2_4 bioconda
iniconfig 2.1.0 pypi_0 pypi
interface-meta 1.3.0 pypi_0 pypi
interlap 0.2.7 pypi_0 pypi
intervaltree 3.1.0 pypi_0 pypi
ipykernel 6.29.5 pyh3099207_0 conda-forge
ipython 9.4.0 pyhfa0c392_0 conda-forge
ipython_pygments_lexers 1.1.1 pyhd8ed1ab_0 conda-forge
ipywidgets 8.1.7 pypi_0 pypi
isoduration 20.11.0 pyhd8ed1ab_1 conda-forge
itsdangerous 2.2.0 pypi_0 pypi
jax 0.6.2 pypi_0 pypi
jaxlib 0.6.2 pypi_0 pypi
jedi 0.19.2 pyhd8ed1ab_1 conda-forge
jinja2 3.1.6 pyhd8ed1ab_0 conda-forge
jiter 0.10.0 pypi_0 pypi
jmespath 1.0.1 pypi_0 pypi
joblib 1.5.1 pypi_0 pypi
jq 1.8.1 h73b1eb8_0 conda-forge
json5 0.12.0 pyhd8ed1ab_0 conda-forge
jsonpatch 1.33 pypi_0 pypi
jsonpointer 3.0.0 py311h38be061_1 conda-forge
jsonschema 4.24.0 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2025.4.1 pyh29332c3_0 conda-forge
jsonschema-with-format-nongpl 4.24.0 hd8ed1ab_0 conda-forge
jupyter 1.1.1 pypi_0 pypi
jupyter-console 6.6.3 pypi_0 pypi
jupyter-lsp 2.2.5 pyhe01879c_2 conda-forge
jupyter_client 8.6.3 pyhd8ed1ab_1 conda-forge
jupyter_core 5.8.1 pyh31011fe_0 conda-forge
jupyter_events 0.12.0 pyh29332c3_0 conda-forge
jupyter_server 2.16.0 pyhe01879c_0 conda-forge
jupyter_server_terminals 0.5.3 pyhd8ed1ab_1 conda-forge
jupyterlab 4.4.4 pyhd8ed1ab_0 conda-forge
jupyterlab-widgets 3.0.15 pypi_0 pypi
jupyterlab_pygments 0.3.0 pyhd8ed1ab_2 conda-forge
jupyterlab_server 2.27.3 pyhd8ed1ab_1 conda-forge
kernel-headers_linux-64 5.14.0 he073ed8_2 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.8 py311hd18a35c_1 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
langchain 0.3.26 pypi_0 pypi
langchain-anthropic 0.3.17 pypi_0 pypi
langchain-aws 0.2.28 pypi_0 pypi
langchain-community 0.3.27 pypi_0 pypi
langchain-core 0.3.69 pypi_0 pypi
langchain-google-genai 2.1.8 pypi_0 pypi
langchain-ollama 0.3.5 pypi_0 pypi
langchain-openai 0.3.28 pypi_0 pypi
langchain-text-splitters 0.3.8 pypi_0 pypi
langgraph 0.3.18 pypi_0 pypi
langgraph-checkpoint 2.1.0 pypi_0 pypi
langgraph-prebuilt 0.1.8 pypi_0 pypi
langgraph-sdk 0.1.73 pypi_0 pypi
langsmith 0.4.6 pypi_0 pypi
lazy-loader 0.4 pypi_0 pypi
lcms2 2.17 h717163a_0 conda-forge
ld_impl_linux-64 2.44 h1423503_1 conda-forge
legacy-api-wrap 1.4.1 pypi_0 pypi
lerc 4.0.0 h0aef613_1 conda-forge
libabseil 20250512.1 cxx17_hba17884_0 conda-forge
libarrow 20.0.0 h94aa55a_14_cpu conda-forge
libarrow-acero 20.0.0 h635bf11_14_cpu conda-forge
libarrow-dataset 20.0.0 h635bf11_14_cpu conda-forge
libarrow-substrait 20.0.0 h3f74fd7_14_cpu conda-forge
libasprintf 0.25.1 h8e693c7_0 conda-forge
libblas 3.9.0 32_h59b9bed_openblas conda-forge
libbrotlicommon 1.1.0 hb9d3cd8_3 conda-forge
libbrotlidec 1.1.0 hb9d3cd8_3 conda-forge
libbrotlienc 1.1.0 hb9d3cd8_3 conda-forge
libcblas 3.9.0 32_he106b2a_openblas conda-forge
libcrc32c 1.1.2 h9c3ff4c_0 conda-forge
libcups 2.3.3 hb8b1518_5 conda-forge
libcurl 8.14.1 h332b0f4_0 conda-forge
libdeflate 1.24 h86f0d12_0 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libev 4.33 hd590300_2 conda-forge
libevent 2.1.12 hf998b51_1 conda-forge
libexpat 2.7.1 hecca717_0 conda-forge
libffi 3.4.6 h2dba641_1 conda-forge
libfreetype 2.13.3 ha770c72_1 conda-forge
libfreetype6 2.13.3 h48d6fc4_1 conda-forge
libgcc 15.1.0 h767d61c_3 conda-forge
libgcc-devel_linux-64 15.1.0 h4c094af_103 conda-forge
libgcc-ng 15.1.0 h69a702a_3 conda-forge
libgettextpo 0.25.1 h5888daf_0 conda-forge
libgfortran 15.1.0 h69a702a_3 conda-forge
libgfortran-ng 15.1.0 h69a702a_3 conda-forge
libgfortran5 15.1.0 hcea5267_3 conda-forge
libglib 2.84.2 h3618099_0 conda-forge
libgomp 15.1.0 h767d61c_3 conda-forge
libgoogle-cloud 2.39.0 hdb79228_0 conda-forge
libgoogle-cloud-storage 2.39.0 hdbdcf42_0 conda-forge
libgrpc 1.73.1 h1e535eb_0 conda-forge
libiconv 1.18 h4ce23a2_1 conda-forge
libidn2 2.3.8 ha4ef2c3_0 conda-forge
libjpeg-turbo 3.1.0 hb9d3cd8_0 conda-forge
liblapack 3.9.0 32_h7ac8fdf_openblas conda-forge
liblzma 5.8.1 hb9d3cd8_2 conda-forge
libnghttp2 1.64.0 h161d5f1_0 conda-forge
libnsl 2.0.1 hb9d3cd8_1 conda-forge
libopenblas 0.3.30 pthreads_h94d23a6_0 conda-forge
libopentelemetry-cpp 1.21.0 hb9b0907_1 conda-forge
libopentelemetry-cpp-headers 1.21.0 ha770c72_1 conda-forge
libparquet 20.0.0 h790f06f_14_cpu conda-forge
libpng 1.6.50 h943b412_0 conda-forge
libprotobuf 6.31.1 h9ef548d_1 conda-forge
libre2-11 2025.06.26 h7064273_1 conda-forge
libsanitizer 15.1.0 h97b714f_3 conda-forge
libsodium 1.0.20 h4ab18f5_0 conda-forge
libsqlite 3.50.2 hee844dc_2 conda-forge
libssh2 1.11.1 hcf80075_0 conda-forge
libstdcxx 15.1.0 h8f9b012_3 conda-forge
libstdcxx-devel_linux-64 15.1.0 h4c094af_103 conda-forge
libstdcxx-ng 15.1.0 h4852527_3 conda-forge
libthrift 0.22.0 h093b73b_0 conda-forge
libtiff 4.7.0 hf01ce69_5 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libutf8proc 2.10.0 h202a827_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libuv 1.51.0 hb9d3cd8_0 conda-forge
libwebp-base 1.6.0 hd42ef1d_0 conda-forge
libxcb 1.17.0 h8a09558_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxml2 2.13.8 h4bc477f_0 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
lifelines 0.30.0 pypi_0 pypi
lightning 2.5.2 pypi_0 pypi
lightning-utilities 0.14.3 pypi_0 pypi
llvmlite 0.44.0 pypi_0 pypi
locket 1.0.0 pypi_0 pypi
loompy 3.0.8 pypi_0 pypi
looseversion 1.1.2 pypi_0 pypi
lxml 6.0.0 pypi_0 pypi
lz4 4.4.4 pypi_0 pypi
lz4-c 1.10.0 h5888daf_1 conda-forge
macs2 2.2.9.1 pypi_0 pypi
mafft 7.526 h4bc722e_0 conda-forge
mageck 0.5.9.5 py311he264feb_6 bioconda
make 4.4.1 hb9d3cd8_2 conda-forge
markdown 3.8.2 pypi_0 pypi
markdown-it-py 3.0.0 pypi_0 pypi
markupsafe 3.0.2 py311h2dc5d0c_1 conda-forge
marshmallow 3.26.1 pypi_0 pypi
matplotlib-base 3.10.3 py311h2b939e6_0 conda-forge
matplotlib-inline 0.1.7 pyhd8ed1ab_1 conda-forge
mdurl 0.1.2 pypi_0 pypi
mistune 3.1.3 pyh29332c3_0 conda-forge
ml-collections 1.1.0 pypi_0 pypi
ml-dtypes 0.5.1 pypi_0 pypi
mmtf-python 1.1.3 pypi_0 pypi
more-itertools 10.7.0 pypi_0 pypi
mpfr 4.2.1 h90cbb55_3 conda-forge
mpmath 1.3.0 pypi_0 pypi
msgpack 1.1.1 pypi_0 pypi
msgpack-numpy 0.4.8 pypi_0 pypi
msprime 1.3.4 pypi_0 pypi
mudata 0.3.2 pypi_0 pypi
multidict 6.6.3 pypi_0 pypi
multipledispatch 1.0.0 pypi_0 pypi
multiprocess 0.70.18 pypi_0 pypi
multiprocessing-on-dill 3.5.0a4 pypi_0 pypi
munkres 1.1.4 pyhd8ed1ab_1 conda-forge
mypy-extensions 1.1.0 pypi_0 pypi
mysql-connector-python 9.4.0 pypi_0 pypi
narwhals 1.47.0 pyhe01879c_0 conda-forge
natsort 8.4.0 pypi_0 pypi
nbclient 0.10.2 pyhd8ed1ab_0 conda-forge
nbconvert-core 7.16.6 pyh29332c3_0 conda-forge
nbformat 5.10.4 pyhd8ed1ab_1 conda-forge
ncbi-vdb 3.2.1 h9948957_0 bioconda
ncls 0.0.70 pypi_0 pypi
ncurses 6.5 h2d0b736_3 conda-forge
ndindex 1.10.0 pypi_0 pypi
nest-asyncio 1.6.0 pyhd8ed1ab_1 conda-forge
netcdf4 1.7.2 pypi_0 pypi
networkx 3.5 pypi_0 pypi
newick 1.10.0 pypi_0 pypi
nlohmann_json 3.12.0 h3f2d84a_0 conda-forge
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setuptools 80.9.0 pyhff2d567_0 conda-forge
sgmllib3k 1.0.0 pypi_0 pypi
shapely 2.1.1 pypi_0 pypi
shellingham 1.5.4 pypi_0 pypi
simplejson 3.20.1 pypi_0 pypi
six 1.17.0 pyhd8ed1ab_0 conda-forge
smmap 5.0.2 pyhd8ed1ab_0 conda-forge
snappy 1.2.1 h8bd8927_1 conda-forge
sniffio 1.3.1 pyhd8ed1ab_1 conda-forge
snowballstemmer 3.0.1 pypi_0 pypi
somacore 1.0.28 pypi_0 pypi
sorted-nearest 0.0.39 pypi_0 pypi
sortedcontainers 2.4.0 pypi_0 pypi
soupsieve 2.7 pyhd8ed1ab_0 conda-forge
sparse 0.17.0 pypi_0 pypi
sphinx 8.2.3 pypi_0 pypi
sphinx-rtd-theme 3.0.2 pypi_0 pypi
sphinxcontrib-applehelp 2.0.0 pypi_0 pypi
sphinxcontrib-devhelp 2.0.0 pypi_0 pypi
sphinxcontrib-htmlhelp 2.1.0 pypi_0 pypi
sphinxcontrib-jquery 4.1 pypi_0 pypi
sphinxcontrib-jsmath 1.0.1 pypi_0 pypi
sphinxcontrib-qthelp 2.0.0 pypi_0 pypi
sphinxcontrib-serializinghtml 2.0.0 pypi_0 pypi
sqlalchemy 2.0.41 pypi_0 pypi
stack_data 0.6.3 pyhd8ed1ab_1 conda-forge
starlette 0.47.1 pypi_0 pypi
statsmodels 0.14.5 pypi_0 pypi
streamlit 1.46.1 pyhd8ed1ab_0 conda-forge
swiglpk 5.0.12 pypi_0 pypi
sympy 1.14.0 pypi_0 pypi
sysroot_linux-64 2.34 h087de78_2 conda-forge
tables 3.10.2 pypi_0 pypi
tabulate 0.9.0 pyhd8ed1ab_2 conda-forge
tblib 3.1.0 pypi_0 pypi
tenacity 9.1.2 pyhd8ed1ab_0 conda-forge
tensorboard 2.20.0 pypi_0 pypi
tensorboard-data-server 0.7.2 pypi_0 pypi
tensorstore 0.1.76 pypi_0 pypi
terminado 0.18.1 pyh0d859eb_0 conda-forge
texttable 1.7.0 pypi_0 pypi
theano-pymc 1.1.2 pypi_0 pypi
threadpoolctl 3.6.0 pypi_0 pypi
tifffile 2025.6.11 pypi_0 pypi
tiktoken 0.9.0 pypi_0 pypi
tiledbsoma 1.17.0 pypi_0 pypi
tinycss2 1.4.0 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_hd72426e_102 conda-forge
tktable 2.10 h8d826fa_7 conda-forge
tokenizers 0.21.2 pypi_0 pypi
toml 0.10.2 pyhd8ed1ab_1 conda-forge
tomli 2.2.1 pyhd8ed1ab_1 conda-forge
tomlkit 0.13.3 pypi_0 pypi
toolz 1.0.0 pypi_0 pypi
torch 2.7.1 pypi_0 pypi
torchmetrics 1.7.4 pypi_0 pypi
torchvision 0.22.1 pypi_0 pypi
tornado 6.5.1 py311h9ecbd09_0 conda-forge
tqdm 4.67.1 pypi_0 pypi
trackpy 0.7 pypi_0 pypi
traitlets 5.14.3 pyhd8ed1ab_1 conda-forge
transformers 4.53.2 pypi_0 pypi
treescope 0.1.9 pypi_0 pypi
trimmomatic 0.39 hdfd78af_2 bioconda
trio 0.30.0 pypi_0 pypi
trio-websocket 0.12.2 pypi_0 pypi
triton 3.3.1 pypi_0 pypi
trnascan-se 2.0.12 pl5321h7b50bb2_2 bioconda
tskit 0.6.4 pypi_0 pypi
typer 0.16.0 pypi_0 pypi
types-python-dateutil 2.9.0.20250708 pyhd8ed1ab_0 conda-forge
typing-extensions 4.14.1 h4440ef1_0 conda-forge
typing-inspect 0.9.0 pypi_0 pypi
typing-inspection 0.4.1 pypi_0 pypi
typing_extensions 4.14.1 pyhe01879c_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_1 conda-forge
tzdata 2025b h78e105d_0 conda-forge
umap-learn 0.5.9.post2 pypi_0 pypi
unicodedata2 16.0.0 py311h9ecbd09_0 conda-forge
uri-template 1.3.0 pyhd8ed1ab_1 conda-forge
urllib3 2.5.0 pyhd8ed1ab_0 conda-forge
uvicorn 0.35.0 pypi_0 pypi
viennarna 2.7.0 pypi_0 pypi
watchdog 6.0.0 py311h38be061_0 conda-forge
wcwidth 0.2.13 pyhd8ed1ab_1 conda-forge
webargs 8.7.0 pypi_0 pypi
webcolors 24.11.1 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_3 conda-forge
websocket-client 1.8.0 pyhd8ed1ab_1 conda-forge
websockets 15.0.1 pypi_0 pypi
werkzeug 3.1.3 pypi_0 pypi
wget 1.21.4 hda4d442_0 conda-forge
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
widgetsnbextension 4.0.14 pypi_0 pypi
wrapt 1.17.2 pypi_0 pypi
wsproto 1.2.0 pypi_0 pypi
xarray 2025.7.1 pypi_0 pypi
xarray-einstats 0.9.1 pypi_0 pypi
xorg-libice 1.1.2 hb9d3cd8_0 conda-forge
xorg-libsm 1.2.6 he73a12e_0 conda-forge
xorg-libx11 1.8.12 h4f16b4b_0 conda-forge
xorg-libxau 1.0.12 hb9d3cd8_0 conda-forge
xorg-libxdmcp 1.1.5 hb9d3cd8_0 conda-forge
xorg-libxext 1.3.6 hb9d3cd8_0 conda-forge
xorg-libxfixes 6.0.1 hb9d3cd8_0 conda-forge
xorg-libxi 1.8.2 hb9d3cd8_0 conda-forge
xorg-libxrandr 1.5.4 hb9d3cd8_0 conda-forge
xorg-libxrender 0.9.12 hb9d3cd8_0 conda-forge
xorg-libxt 1.3.1 hb9d3cd8_0 conda-forge
xorg-libxtst 1.2.5 hb9d3cd8_3 conda-forge
xyzservices 2025.4.0 pyhd8ed1ab_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yarl 1.20.1 pypi_0 pypi
zarr 3.1.0 pypi_0 pypi
zeromq 4.3.5 h3b0a872_7 conda-forge
zict 3.0.0 pypi_0 pypi
zipp 3.23.0 pyhd8ed1ab_0 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zstandard 0.23.0 pypi_0 pypi
zstd 1.5.7 hb8e6e7a_2 conda-forge"
if that also didnt work just do it manuelly for rdkit,
conda activate biomni_e1
pip install rdkit
Hey. I really think we're gonna see a lot of issues raised like this (I raised one myself) if the env install is kept seperate. I know the argument was that install is long, so updating is faster, but it is much faster when things are already installed and auto skipped, unless they are needed (in which case they are needed...).
I'd recommend reconsidering combining the code and the env install process.
@evolu8 Yes i do agree, I added some changes in this issue #83 in which i suggested letting Conda solve all these problems, But mainly we need to check the OS of the machine since ARM chips from apple Silicon can not install these packages such as mageck. It will require osx-64 emulation on Apple Silicon.
Also, i think for the CLI tools since they require environment variable change, we can set them up with Bash Script but inside the Conda environment. so that for example HOMER or MUSCLE is only on the PATH when you activate biomni_e1 environment
name: biomni_e1
channels:
- conda-forge
- bioconda
- defaults
dependencies:
# Python Core
- python=3.11
- pip
# Python Libraries (from environment.yml & bio_env.yml)
- numpy>=2.0
- pandas
- matplotlib
- scipy
- statsmodels
- scikit-learn
- gradio
- langchain
- langgraph
- langchain_openai
- langchain_anthropic
- langchain_community
- langchain-google-genai
- langchain_ollama
- openai
- beautifulsoup4
- lxml
- tqdm
- seaborn
- networkx
- requests
- pyyaml
- jupyter
- transformers
- sentencepiece
- python-dotenv
- biopython
- scanpy
- pybedtools # Solves the zlib issue
- gseapy
- mageck # Will require osx-64 emulation on Apple Silicon
- macs2
- scikit-image
- anndata
# R Core & Packages (from install_r_packages.R)
- r-base>=4.3
- r-essentials
- r-ggplot2
- r-lme4
- r-dplyr
- r-tidyr
- r-readr
- r-stringr
- r-matrix
- r-rcpp
- r-devtools
- r-remotes
- r-harmony
- bioconductor-deseq2
- bioconductor-flowcore
- bioconductor-edger
- bioconductor-limma
- r-wgcna
- bioconductor-clusterprofiler
# CLI Tools (from bio_env.yml & install_cli_tools.sh)
- blast
- samtools
- bowtie2
- bwa
- bedtools
- fastqc
- trimmomatic
- mafft
- plink2
- iqtree
- gcta
- muscle
- homer
# Note: FastTree might need manual handling if a Conda package isn't suitable
Hi! Thanks for pitching in! As our environment is massive and highly complex (with R, Python, and CLI), I am thinking combining them with pip install biomni is hard. Especially, we have only tested it on linux ubuntu system. I believe it will have issues in other system. But if you know an easy way to manage this - would love to hear your ideas.
Currently, for additional packages in a new version, we have a separate new_software_vXXX.sh to install.
