CellBender をテンプレートにして作成
[
トップ
] [
新規
|
一覧
|
検索
|
最終更新
|
ヘルプ
|
ログイン
]
開始行:
ドキュメント [[https://cellbender.readthedocs.io/en/lates...
github [[https://github.com/broadinstitute/CellBender>+ht...
pipy [[https://pypi.org/project/cellbender/>+https://pypi...
#code(nonumber){{
git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
pyenv install miniforge3-26.3.2-1
source /apps/pyenv/versions/miniforge3-26.3.2-1/etc/profi...
conda update conda
(既に環境があるなら)
source /apps/pyenv/versions/miniforge3-26.3.2-1/etc/profi...
}}
#code(nonumber){{
[root@r9 ~]# cat /etc/redhat-release
Rocky Linux release 9.7 (Blue Onyx)
[root@r9 ~]# cat /proc/driver/nvidia/version
NVRM version: NVIDIA UNIX Open Kernel Module for x86_64 ...
GCC version: gcc version 11.5.0 20240719 (Red Hat 11.5.0...
[root@r9 ~]# nvidia-smi -L
GPU 0: NVIDIA RTX PRO 2000 Blackwell (UUID: GPU-40660e37-...
[root@r9 ~]#
}}
#code(nonumber){{
[root@r9 ~]# conda create -n cellbender python=3.12
[root@r9 ~]# conda activate cellbender
(cellbender) [root@r9 ~]#
(cellbender) [root@r9 ~]# conda install -c anaconda pytab...
(cellbender) [root@r9 ~]# pip install torch
(cellbender) [root@r9 ~]# conda list
# packages in environment at /apps/pyenv/versions/minifor...
#
# Name Version Build ...
_openmp_mutex 4.5 20_gnu ...
aws-c-auth 0.10.1 h47b2149_0 ...
aws-c-cal 0.9.13 h1b28b03_0 ...
aws-c-common 0.12.6 h47b2149_0 ...
aws-c-compression 0.3.2 h47b2149_0 ...
aws-c-http 0.10.13 h47b2149_0 ...
aws-c-io 0.26.3 h1b29dbc_0 ...
aws-c-s3 0.12.0 h1b28b03_1 ...
aws-c-sdkutils 0.2.4 h47b2149_2 ...
aws-checksums 0.2.10 h47b2149_0 ...
blas 1.0 openblas ...
blosc 1.21.6 he440d0b_1 ...
bzip2 1.0.8 hda65f42_9 ...
c-ares 1.34.6 hd44998d_0 ...
c-blosc2 2.22.0 hc31b594_1 ...
ca-certificates 2026.5.20 hbd8a1cb_0 ...
cuda-bindings 13.3.1 pypi_0 ...
cuda-pathfinder 1.5.5 pypi_0 ...
cuda-toolkit 13.0.2 pypi_0 ...
filelock 3.29.1 pypi_0 ...
fsspec 2026.4.0 pypi_0 ...
gettext 0.25.1 h92eb808_0 ...
gettext-tools 0.25.1 h6a67909_0 ...
hdf5 2.0.0 h91801a2_3 ...
icu 78.3 h84d19a5_0 ...
jansson 2.15.0 hbcba0ee_0 ...
jinja2 3.1.6 pypi_0 ...
ld_impl_linux-64 2.45.1 default_hbd61...
libasprintf 0.25.1 hf2ab22a_0 ...
libasprintf-devel 0.25.1 hf2ab22a_0 ...
libbrotlicommon 1.2.0 h32cd6e7_0 ...
libbrotlidec 1.2.0 ha2c5f68_0 ...
libbrotlienc 1.2.0 h2e96acb_0 ...
libcurl 8.20.0 hd8fa685_1 ...
libev 4.33 h7f8727e_1 ...
libexpat 2.8.1 hecca717_0 ...
libffi 3.5.2 h3435931_0 ...
libgcc 15.2.0 he0feb66_19 ...
libgcc-ng 15.2.0 h69a702a_19 ...
libgettextpo 0.25.1 hf2ab22a_0 ...
libgettextpo-devel 0.25.1 hf2ab22a_0 ...
libgfortran 15.2.0 h166f726_7 ...
libgfortran5 15.2.0 hc633d37_7 ...
libgomp 15.2.0 he0feb66_19 ...
libiconv 1.18 h75a1612_0 ...
libidn2 2.3.8 hf80d704_0 ...
libkrb5 1.22.1 h869c75e_1 ...
liblzma 5.8.3 hb03c661_0 ...
liblzma-devel 5.8.3 hb03c661_0 ...
libnghttp2 1.69.0 hc59f8b6_0 ...
libnsl 2.0.1 hb9d3cd8_1 ...
libopenblas 0.3.31 hf7dbefb_2 ...
libsqlite 3.53.2 h0c1763c_0 ...
libssh2 1.11.1 hcf80075_0 ...
libstdcxx 15.2.0 h934c35e_19 ...
libstdcxx-ng 15.2.0 hdf11a46_19 ...
libunistring 1.4.2 h34b0ebb_0 ...
libuuid 2.42.1 h5347b49_0 ...
libxcrypt 4.4.36 hd590300_1 ...
libxml2 2.14.6 hf2a51f9_1 ...
libzlib 1.3.2 h25fd6f3_2 ...
lmdb 0.9.31 hb25bd0a_0 ...
lz4-c 1.10.0 h5888daf_1 ...
lzo 2.10 h7b6447c_2 ...
markupsafe 3.0.3 pypi_0 ...
mpmath 1.3.0 pypi_0 ...
ncurses 6.6 hdb14827_0 ...
networkx 3.6.1 pypi_0 ...
numexpr 2.14.1 py312h5c6250f...
numpy 2.4.6 py312h35deafb...
numpy-base 2.4.6 py312h4bc27c9...
nvidia-cublas 13.1.1.3 pypi_0 ...
nvidia-cuda-cupti 13.0.85 pypi_0 ...
nvidia-cuda-nvrtc 13.0.88 pypi_0 ...
nvidia-cuda-runtime 13.0.96 pypi_0 ...
nvidia-cudnn-cu13 9.20.0.48 pypi_0 ...
nvidia-cufft 12.0.0.61 pypi_0 ...
nvidia-cufile 1.15.1.6 pypi_0 ...
nvidia-curand 10.4.0.35 pypi_0 ...
nvidia-cusolver 12.0.4.66 pypi_0 ...
nvidia-cusparse 12.6.3.3 pypi_0 ...
nvidia-cusparselt-cu13 0.8.1 pypi_0 ...
nvidia-nccl-cu13 2.29.7 pypi_0 ...
nvidia-nvjitlink 13.0.88 pypi_0 ...
nvidia-nvshmem-cu13 3.4.5 pypi_0 ...
nvidia-nvtx 13.0.85 pypi_0 ...
openssl 3.6.2 h35e630c_0 ...
packaging 26.2 pyhc364b38_0 ...
pip 26.1.2 pyh8b19718_0 ...
py-cpuinfo 9.0.0 py312h06a4308...
pytables 3.11.1 py312h4db2897...
python 3.12.13 hd63d673_0_cp...
readline 8.3 h853b02a_0 ...
s2n 1.6.2 h02aa81b_0 ...
setuptools 81.0.0 pypi_0 ...
snappy 1.2.1 h6a678d5_0 ...
sympy 1.14.0 pypi_0 ...
tk 8.6.13 noxft_h366c99...
torch 2.12.0 pypi_0 ...
triton 3.7.0 pypi_0 ...
typing-extensions 4.15.0 py312h06a4308...
typing_extensions 4.15.0 py312h06a4308...
tzdata 2025c hc9c84f9_1 ...
wheel 0.47.0 pyhd8ed1ab_0 ...
xz 5.8.3 ha02ee65_0 ...
xz-gpl-tools 5.8.3 ha02ee65_0 ...
xz-tools 5.8.3 hb03c661_0 ...
zlib 1.3.2 h25fd6f3_2 ...
zlib-ng 2.3.3 hcff5ade_0 ...
zstd 1.5.7 hb78ec9c_6 ...
(cellbender) [root@r9 ~]#
}}
#code(nonumber){{
(cellbender) [root@r9 ~]# python
Python 3.12.13 | packaged by conda-forge | (main, Mar 5 ...
Type "help", "copyright", "credits" or "license" for more...
>>> import torch
>>> print(torch.cuda.is_available())
True
>>> print(torch.cuda.get_device_name())
NVIDIA RTX PRO 2000 Blackwell
>>> quit();
(cellbender) [root@r9 ~]#
}}
#code(nonumber){{
(cellbender) [root@r9 ~]# cd /apps
(cellbender) [root@r9 apps]# git clone https://github.com...
(cellbender) [root@r9 apps]# pip install -e CellBender
(cellbender) [root@r9 apps]# conda deactivate
[root@r9 ~]#
}}
「/apps/modulefiles/CellBender」
#code(nonumber){{
#%Module
set root /apps/pyenv/versions/miniforge3-26.3....
prepend-path PATH $root/bin
prepend-path LD_LIBRARY_PATH $root/lib
}}
#code(nonumber){{
[saber@r9 ~]$ module load CellBender
[saber@r9 ~]$ mkdir test
[saber@r9 ~]$ cd test/
[saber@r9 test]$ git clone https://github.com/broadinstit...
[saber@r9 test]$ cd CellBender/
[saber@r9 CellBender]$ cd examples/remove_background/
[saber@r9 remove_background]$ python generate_tiny_10x_da...
Downloading heart10k (CellRanger 3.0.0, v3 Chemistry)...
--2026-06-08 20:15:30-- https://cf.10xgenomics.com/sampl...
Resolving cf.10xgenomics.com (cf.10xgenomics.com)... 104....
Connecting to cf.10xgenomics.com (cf.10xgenomics.com)|104...
HTTP request sent, awaiting response... 200 OK
Length: 167177525 (159M) [binary/octet-stream]
Saving to: ‘heart10k_raw_feature_bc_matrix.h5’
heart10k_raw_feature_bc_matrix.h5 100%[=============...
2026-06-08 20:15:37 (28.0 MB/s) - ‘heart10k_raw_feature_b...
Loading the dataset...
/apps/pyenv/versions/miniforge3-26.3.2-1/envs/cellbender/...
return fn(*args_all, **kw)
Raw dataset size (6794880, 31053)
Trimming heart10k (CellRanger 3.0.0, v3 Chemistry)...
Number of genes in the trimmed dataset: 100
Number of barcodes in the trimmed dataset: 37760
Expected number of cells in the trimmed dataset: 500
AnnData object with n_obs × n_vars = 37760 × 100
var: 'gene_id', 'genome', 'feature_type'
uns: 'cellranger_version'
Saving the trimmed dataset as tiny_raw_feature_bc_matrix....
Done!
[saber@r9 remove_background]$
[saber@r9 remove_background]$ cellbender remove-backgroun...
--input tiny_raw_feature_bc_matrix.h5ad \
--output tiny_output.h5 \
--expected-cells 500 \
--total-droplets-included 2000 \
--cuda
:
:
[saber@r9 remove_background]$ ls -lrt
total 205908
-rw-r--r-- 1 saber saber 167177525 Nov 15 2018 heart10k_...
-rwxr-xr-x 1 saber saber 3058 Jun 8 20:07 generate_...
-rw-r--r-- 1 saber saber 14660728 Jun 8 20:15 tiny_raw_...
-rw-r--r-- 1 saber saber 2134377 Jun 8 20:17 tiny_outp...
-rw-r--r-- 1 saber saber 24664467 Jun 8 20:17 ckpt.tar.gz
-rw-r--r-- 1 saber saber 118891 Jun 8 20:17 tiny_outp...
-rw-r--r-- 1 saber saber 12369 Jun 8 20:17 tiny_outp...
-rw-r--r-- 1 saber saber 940820 Jun 8 20:17 tiny_outp...
-rw-r--r-- 1 saber saber 351137 Jun 8 20:17 tiny_outp...
-rw-r--r-- 1 saber saber 573 Jun 8 20:17 tiny_outp...
-rw-r--r-- 1 saber saber 740831 Jun 8 20:17 tiny_outp...
-rw-r--r-- 1 saber saber 18246 Jun 8 20:17 tiny_outp...
[saber@r9 remove_background]$
}}
終了行:
ドキュメント [[https://cellbender.readthedocs.io/en/lates...
github [[https://github.com/broadinstitute/CellBender>+ht...
pipy [[https://pypi.org/project/cellbender/>+https://pypi...
#code(nonumber){{
git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
pyenv install miniforge3-26.3.2-1
source /apps/pyenv/versions/miniforge3-26.3.2-1/etc/profi...
conda update conda
(既に環境があるなら)
source /apps/pyenv/versions/miniforge3-26.3.2-1/etc/profi...
}}
#code(nonumber){{
[root@r9 ~]# cat /etc/redhat-release
Rocky Linux release 9.7 (Blue Onyx)
[root@r9 ~]# cat /proc/driver/nvidia/version
NVRM version: NVIDIA UNIX Open Kernel Module for x86_64 ...
GCC version: gcc version 11.5.0 20240719 (Red Hat 11.5.0...
[root@r9 ~]# nvidia-smi -L
GPU 0: NVIDIA RTX PRO 2000 Blackwell (UUID: GPU-40660e37-...
[root@r9 ~]#
}}
#code(nonumber){{
[root@r9 ~]# conda create -n cellbender python=3.12
[root@r9 ~]# conda activate cellbender
(cellbender) [root@r9 ~]#
(cellbender) [root@r9 ~]# conda install -c anaconda pytab...
(cellbender) [root@r9 ~]# pip install torch
(cellbender) [root@r9 ~]# conda list
# packages in environment at /apps/pyenv/versions/minifor...
#
# Name Version Build ...
_openmp_mutex 4.5 20_gnu ...
aws-c-auth 0.10.1 h47b2149_0 ...
aws-c-cal 0.9.13 h1b28b03_0 ...
aws-c-common 0.12.6 h47b2149_0 ...
aws-c-compression 0.3.2 h47b2149_0 ...
aws-c-http 0.10.13 h47b2149_0 ...
aws-c-io 0.26.3 h1b29dbc_0 ...
aws-c-s3 0.12.0 h1b28b03_1 ...
aws-c-sdkutils 0.2.4 h47b2149_2 ...
aws-checksums 0.2.10 h47b2149_0 ...
blas 1.0 openblas ...
blosc 1.21.6 he440d0b_1 ...
bzip2 1.0.8 hda65f42_9 ...
c-ares 1.34.6 hd44998d_0 ...
c-blosc2 2.22.0 hc31b594_1 ...
ca-certificates 2026.5.20 hbd8a1cb_0 ...
cuda-bindings 13.3.1 pypi_0 ...
cuda-pathfinder 1.5.5 pypi_0 ...
cuda-toolkit 13.0.2 pypi_0 ...
filelock 3.29.1 pypi_0 ...
fsspec 2026.4.0 pypi_0 ...
gettext 0.25.1 h92eb808_0 ...
gettext-tools 0.25.1 h6a67909_0 ...
hdf5 2.0.0 h91801a2_3 ...
icu 78.3 h84d19a5_0 ...
jansson 2.15.0 hbcba0ee_0 ...
jinja2 3.1.6 pypi_0 ...
ld_impl_linux-64 2.45.1 default_hbd61...
libasprintf 0.25.1 hf2ab22a_0 ...
libasprintf-devel 0.25.1 hf2ab22a_0 ...
libbrotlicommon 1.2.0 h32cd6e7_0 ...
libbrotlidec 1.2.0 ha2c5f68_0 ...
libbrotlienc 1.2.0 h2e96acb_0 ...
libcurl 8.20.0 hd8fa685_1 ...
libev 4.33 h7f8727e_1 ...
libexpat 2.8.1 hecca717_0 ...
libffi 3.5.2 h3435931_0 ...
libgcc 15.2.0 he0feb66_19 ...
libgcc-ng 15.2.0 h69a702a_19 ...
libgettextpo 0.25.1 hf2ab22a_0 ...
libgettextpo-devel 0.25.1 hf2ab22a_0 ...
libgfortran 15.2.0 h166f726_7 ...
libgfortran5 15.2.0 hc633d37_7 ...
libgomp 15.2.0 he0feb66_19 ...
libiconv 1.18 h75a1612_0 ...
libidn2 2.3.8 hf80d704_0 ...
libkrb5 1.22.1 h869c75e_1 ...
liblzma 5.8.3 hb03c661_0 ...
liblzma-devel 5.8.3 hb03c661_0 ...
libnghttp2 1.69.0 hc59f8b6_0 ...
libnsl 2.0.1 hb9d3cd8_1 ...
libopenblas 0.3.31 hf7dbefb_2 ...
libsqlite 3.53.2 h0c1763c_0 ...
libssh2 1.11.1 hcf80075_0 ...
libstdcxx 15.2.0 h934c35e_19 ...
libstdcxx-ng 15.2.0 hdf11a46_19 ...
libunistring 1.4.2 h34b0ebb_0 ...
libuuid 2.42.1 h5347b49_0 ...
libxcrypt 4.4.36 hd590300_1 ...
libxml2 2.14.6 hf2a51f9_1 ...
libzlib 1.3.2 h25fd6f3_2 ...
lmdb 0.9.31 hb25bd0a_0 ...
lz4-c 1.10.0 h5888daf_1 ...
lzo 2.10 h7b6447c_2 ...
markupsafe 3.0.3 pypi_0 ...
mpmath 1.3.0 pypi_0 ...
ncurses 6.6 hdb14827_0 ...
networkx 3.6.1 pypi_0 ...
numexpr 2.14.1 py312h5c6250f...
numpy 2.4.6 py312h35deafb...
numpy-base 2.4.6 py312h4bc27c9...
nvidia-cublas 13.1.1.3 pypi_0 ...
nvidia-cuda-cupti 13.0.85 pypi_0 ...
nvidia-cuda-nvrtc 13.0.88 pypi_0 ...
nvidia-cuda-runtime 13.0.96 pypi_0 ...
nvidia-cudnn-cu13 9.20.0.48 pypi_0 ...
nvidia-cufft 12.0.0.61 pypi_0 ...
nvidia-cufile 1.15.1.6 pypi_0 ...
nvidia-curand 10.4.0.35 pypi_0 ...
nvidia-cusolver 12.0.4.66 pypi_0 ...
nvidia-cusparse 12.6.3.3 pypi_0 ...
nvidia-cusparselt-cu13 0.8.1 pypi_0 ...
nvidia-nccl-cu13 2.29.7 pypi_0 ...
nvidia-nvjitlink 13.0.88 pypi_0 ...
nvidia-nvshmem-cu13 3.4.5 pypi_0 ...
nvidia-nvtx 13.0.85 pypi_0 ...
openssl 3.6.2 h35e630c_0 ...
packaging 26.2 pyhc364b38_0 ...
pip 26.1.2 pyh8b19718_0 ...
py-cpuinfo 9.0.0 py312h06a4308...
pytables 3.11.1 py312h4db2897...
python 3.12.13 hd63d673_0_cp...
readline 8.3 h853b02a_0 ...
s2n 1.6.2 h02aa81b_0 ...
setuptools 81.0.0 pypi_0 ...
snappy 1.2.1 h6a678d5_0 ...
sympy 1.14.0 pypi_0 ...
tk 8.6.13 noxft_h366c99...
torch 2.12.0 pypi_0 ...
triton 3.7.0 pypi_0 ...
typing-extensions 4.15.0 py312h06a4308...
typing_extensions 4.15.0 py312h06a4308...
tzdata 2025c hc9c84f9_1 ...
wheel 0.47.0 pyhd8ed1ab_0 ...
xz 5.8.3 ha02ee65_0 ...
xz-gpl-tools 5.8.3 ha02ee65_0 ...
xz-tools 5.8.3 hb03c661_0 ...
zlib 1.3.2 h25fd6f3_2 ...
zlib-ng 2.3.3 hcff5ade_0 ...
zstd 1.5.7 hb78ec9c_6 ...
(cellbender) [root@r9 ~]#
}}
#code(nonumber){{
(cellbender) [root@r9 ~]# python
Python 3.12.13 | packaged by conda-forge | (main, Mar 5 ...
Type "help", "copyright", "credits" or "license" for more...
>>> import torch
>>> print(torch.cuda.is_available())
True
>>> print(torch.cuda.get_device_name())
NVIDIA RTX PRO 2000 Blackwell
>>> quit();
(cellbender) [root@r9 ~]#
}}
#code(nonumber){{
(cellbender) [root@r9 ~]# cd /apps
(cellbender) [root@r9 apps]# git clone https://github.com...
(cellbender) [root@r9 apps]# pip install -e CellBender
(cellbender) [root@r9 apps]# conda deactivate
[root@r9 ~]#
}}
「/apps/modulefiles/CellBender」
#code(nonumber){{
#%Module
set root /apps/pyenv/versions/miniforge3-26.3....
prepend-path PATH $root/bin
prepend-path LD_LIBRARY_PATH $root/lib
}}
#code(nonumber){{
[saber@r9 ~]$ module load CellBender
[saber@r9 ~]$ mkdir test
[saber@r9 ~]$ cd test/
[saber@r9 test]$ git clone https://github.com/broadinstit...
[saber@r9 test]$ cd CellBender/
[saber@r9 CellBender]$ cd examples/remove_background/
[saber@r9 remove_background]$ python generate_tiny_10x_da...
Downloading heart10k (CellRanger 3.0.0, v3 Chemistry)...
--2026-06-08 20:15:30-- https://cf.10xgenomics.com/sampl...
Resolving cf.10xgenomics.com (cf.10xgenomics.com)... 104....
Connecting to cf.10xgenomics.com (cf.10xgenomics.com)|104...
HTTP request sent, awaiting response... 200 OK
Length: 167177525 (159M) [binary/octet-stream]
Saving to: ‘heart10k_raw_feature_bc_matrix.h5’
heart10k_raw_feature_bc_matrix.h5 100%[=============...
2026-06-08 20:15:37 (28.0 MB/s) - ‘heart10k_raw_feature_b...
Loading the dataset...
/apps/pyenv/versions/miniforge3-26.3.2-1/envs/cellbender/...
return fn(*args_all, **kw)
Raw dataset size (6794880, 31053)
Trimming heart10k (CellRanger 3.0.0, v3 Chemistry)...
Number of genes in the trimmed dataset: 100
Number of barcodes in the trimmed dataset: 37760
Expected number of cells in the trimmed dataset: 500
AnnData object with n_obs × n_vars = 37760 × 100
var: 'gene_id', 'genome', 'feature_type'
uns: 'cellranger_version'
Saving the trimmed dataset as tiny_raw_feature_bc_matrix....
Done!
[saber@r9 remove_background]$
[saber@r9 remove_background]$ cellbender remove-backgroun...
--input tiny_raw_feature_bc_matrix.h5ad \
--output tiny_output.h5 \
--expected-cells 500 \
--total-droplets-included 2000 \
--cuda
:
:
[saber@r9 remove_background]$ ls -lrt
total 205908
-rw-r--r-- 1 saber saber 167177525 Nov 15 2018 heart10k_...
-rwxr-xr-x 1 saber saber 3058 Jun 8 20:07 generate_...
-rw-r--r-- 1 saber saber 14660728 Jun 8 20:15 tiny_raw_...
-rw-r--r-- 1 saber saber 2134377 Jun 8 20:17 tiny_outp...
-rw-r--r-- 1 saber saber 24664467 Jun 8 20:17 ckpt.tar.gz
-rw-r--r-- 1 saber saber 118891 Jun 8 20:17 tiny_outp...
-rw-r--r-- 1 saber saber 12369 Jun 8 20:17 tiny_outp...
-rw-r--r-- 1 saber saber 940820 Jun 8 20:17 tiny_outp...
-rw-r--r-- 1 saber saber 351137 Jun 8 20:17 tiny_outp...
-rw-r--r-- 1 saber saber 573 Jun 8 20:17 tiny_outp...
-rw-r--r-- 1 saber saber 740831 Jun 8 20:17 tiny_outp...
-rw-r--r-- 1 saber saber 18246 Jun 8 20:17 tiny_outp...
[saber@r9 remove_background]$
}}
ページ名:
1
![[PukiWiki]](image/picc.png "[PukiWiki]")
