git clone https://github.com/singleron-RD/CeleScope.git
cd CeleScope
source ~/miniconda3/bin/activate
conda create -n celescope -y --file conda_pkgs.txt
conda activate celescope
pip install celescope --default-timeout=100 -i https://pypi.tuna.tsinghua.edu.cn/simple
測(cè)試
source ~/miniconda3/bin/activate
conda activate celescope
celescope --help
顯示報(bào)錯(cuò)：
Traceback (most recent call last):
File "/work/home/acwnw4bl7y/miniconda3/envs/celescope/bin/celescope", line 5, in <module>
from celescope.celescope import main
File "/work/home/acwnw4bl7y/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/celescope.py", line 14, in <module>
from celescope.tools import utils
File "/work/home/acwnw4bl7y/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 18, in <module>
import pysam
File "/work/home/acwnw4bl7y/miniconda3/envs/celescope/lib/python3.9/site-packages/pysam/__init__.py", line 4, in <module>
from pysam.libchtslib import *
ImportError: libcrypto.so.3: cannot open shared object file: No such file or directory
Traceback (most recent call last):
File "/work/home/acwnw4bl7y/miniconda3/envs/celescope/bin/celescope", line 5, in <module>
from celescope.celescope import main
File "/work/home/acwnw4bl7y/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/celescope.py", line 14, in <module>
from celescope.tools import utils
File "/work/home/acwnw4bl7y/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 18, in <module>
import pysam
File "/work/home/acwnw4bl7y/miniconda3/envs/celescope/lib/python3.9/site-packages/pysam/__init__.py", line 4, in <module>
from pysam.libchtslib import *
ImportError: libcrypto.so.3: cannot open shared object file: No such file or directory
Traceback (most recent call last):
File "/work/home/acwnw4bl7y/miniconda3/envs/celescope/bin/celescope", line 5, in <module>
from celescope.celescope import main
File "/work/home/acwnw4bl7y/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/celescope.py", line 14, in <module>
from celescope.tools import utils
File "/work/home/acwnw4bl7y/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 18, in <module>
import pysam
File "/work/home/acwnw4bl7y/miniconda3/envs/celescope/lib/python3.9/site-packages/pysam/__init__.py", line 4, in <module>
from pysam.libchtslib import *
ImportError: libcrypto.so.3: cannot open shared object file: No such file or directory
提示找不到 libcrypto.so.3嘀倒，重新安裝openssl
conda search openssl=3.0.14
提示不兼容
Loading channels: done
# Name Version Build Channel
openssl 3.0.14 h5eee18b_0 pkgs/main
(celescope) [acwnw4bl7y@tylogin02 ~]$ conda install openssl=3.0.14
Channels:
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
- defaults
- conda-forge
- bioconda
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: failed
LibMambaUnsatisfiableError: Encountered problems while solving:
- package htslib-1.17-h6bc39ce_1 requires openssl >=1.1.1t,<1.1.2a, but none of the providers can be installed
Could not solve for environment specs
The following packages are incompatible
├─ openssl 3.0.14** is requested and can be installed;
└─ star 2.7.11a.* is not installable because it requires
└─ htslib >=1.17,<1.22.0a0 but there are no viable options
├─ htslib 1.17 would require
│ └─ openssl >=1.1.1t,<1.1.2a , which conflicts with any installable versions previously reported;
├─ htslib 1.17 would require
│ └─ openssl >=3.1.0,<4.0a0 , which conflicts with any installable versions previously reported;
├─ htslib 1.18 would require
│ └─ openssl >=3.1.1,<4.0a0 , which conflicts with any installable versions previously reported;
├─ htslib [1.19|1.19.1] would require
│ └─ openssl >=3.2.0,<4.0a0 , which conflicts with any installable versions previously reported;
├─ htslib [1.19.1|1.20] would require
│ └─ openssl >=3.2.1,<4.0a0 , which conflicts with any installable versions previously reported;
├─ htslib 1.20 would require
│ └─ openssl >=3.3.0,<4.0a0 , which conflicts with any installable versions previously reported;
├─ htslib 1.20 would require
│ └─ openssl >=3.3.1,<4.0a0 , which conflicts with any installable versions previously reported;
└─ htslib 1.21 would require
└─ openssl >=3.3.2,<4.0a0 , which conflicts with any installable versions previously reported.```
主要是和htslib不兼容贞谓，安裝指定版本的htslib
conda install htslib=1.18
Channels:
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
- defaults
- conda-forge
- bioconda
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /work/home/acwnw4bl7y/miniconda3/envs/celescope
added / updated specs:
- htslib=1.18
The following packages will be downloaded:
package | build
---------------------------|-----------------
alsa-lib-1.2.7.2 | h166bdaf_0 581 KB conda-forge
cairo-1.16.0 | hb05425b_5 1.2 MB
fontconfig-2.14.1 | h4c34cd2_2 281 KB
gatk4-4.5.0.0 | py36hdfd78af_0 396.9 MB bioconda
glib-2.78.4 | h6a678d5_0 508 KB
glib-tools-2.78.4 | h6a678d5_0 115 KB
harfbuzz-5.3.0 | h418a68e_0 2.2 MB conda-forge
htslib-1.18 | h81da01d_0 2.4 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
icu-70.1 | h27087fc_0 13.5 MB conda-forge
krb5-1.21.3 | h143b758_0 1.3 MB
libcups-2.3.3 | h4637d8d_4 4.3 MB conda-forge
libcurl-8.4.0 | hca28451_0 377 KB conda-forge
libdeflate-1.21 | h4bc722e_0 69 KB conda-forge
libglib-2.78.4 | hdc74915_0 1.5 MB
libiconv-1.17 | hd590300_2 689 KB conda-forge
libtiff-4.2.0 | hecacb30_2 466 KB
libuuid-1.41.5 | h5eee18b_0 27 KB
libxml2-2.10.3 | hca2bb57_4 697 KB conda-forge
openjdk-17.0.3 | hea3dc9f_3 172.5 MB conda-forge
openssl-3.3.2 | hb9d3cd8_0 2.8 MB conda-forge
xorg-fixesproto-5.0 | hb9d3cd8_1003 11 KB conda-forge
xorg-inputproto-2.3.2 | hb9d3cd8_1003 22 KB conda-forge
xorg-kbproto-1.0.7 | hb9d3cd8_1003 30 KB conda-forge
xorg-libx11-1.8.9 | h8ee46fc_0 809 KB conda-forge
xorg-libxext-1.3.4 | h0b41bf4_2 49 KB conda-forge
xorg-libxfixes-5.0.3 | h7f98852_1004 18 KB conda-forge
xorg-libxi-1.7.10 | h4bc722e_1 46 KB conda-forge
xorg-libxrender-0.9.11 | hd590300_0 37 KB conda-forge
xorg-libxtst-1.2.5 | h4bc722e_0 32 KB conda-forge
xorg-recordproto-1.14.2 | hb9d3cd8_1003 10 KB conda-forge
xorg-renderproto-0.11.1 | hb9d3cd8_1003 12 KB conda-forge
xorg-xextproto-7.3.0 | hb9d3cd8_1004 30 KB conda-forge
xorg-xproto-7.0.31 | h27cfd23_1007 73 KB
------------------------------------------------------------
Total: 603.4 MB
The following NEW packages will be INSTALLED:
alsa-lib conda-forge/linux-64::alsa-lib-1.2.7.2-h166bdaf_0
cairo pkgs/main/linux-64::cairo-1.16.0-hb05425b_5
font-ttf-dejavu-s~ pkgs/main/noarch::font-ttf-dejavu-sans-mono-2.37-hd3eb1b0_0
font-ttf-inconsol~ pkgs/main/noarch::font-ttf-inconsolata-2.001-hcb22688_0
font-ttf-source-c~ pkgs/main/noarch::font-ttf-source-code-pro-2.030-hd3eb1b0_0
font-ttf-ubuntu pkgs/main/noarch::font-ttf-ubuntu-0.83-h8b1ccd4_0
fontconfig pkgs/main/linux-64::fontconfig-2.14.1-h4c34cd2_2
fonts-anaconda pkgs/main/noarch::fonts-anaconda-1-h8fa9717_0
fonts-conda-ecosy~ pkgs/main/noarch::fonts-conda-ecosystem-1-hd3eb1b0_0
giflib pkgs/main/linux-64::giflib-5.2.1-h5eee18b_3
glib-tools pkgs/main/linux-64::glib-tools-2.78.4-h6a678d5_0
graphite2 pkgs/main/linux-64::graphite2-1.3.14-h295c915_1
harfbuzz conda-forge/linux-64::harfbuzz-5.3.0-h418a68e_0
icu conda-forge/linux-64::icu-70.1-h27087fc_0
jpeg pkgs/main/linux-64::jpeg-9e-h5eee18b_3
lcms2 pkgs/main/linux-64::lcms2-2.12-h3be6417_0
libcups conda-forge/linux-64::libcups-2.3.3-h4637d8d_4
libglib pkgs/main/linux-64::libglib-2.78.4-hdc74915_0
libiconv conda-forge/linux-64::libiconv-1.17-hd590300_2
libtiff pkgs/main/linux-64::libtiff-4.2.0-hecacb30_2
libuuid pkgs/main/linux-64::libuuid-1.41.5-h5eee18b_0
libwebp-base pkgs/main/linux-64::libwebp-base-1.3.2-h5eee18b_0
libxml2 conda-forge/linux-64::libxml2-2.10.3-hca2bb57_4
lz4-c pkgs/main/linux-64::lz4-c-1.9.4-h6a678d5_1
pcre2 pkgs/main/linux-64::pcre2-10.42-hebb0a14_1
pixman pkgs/main/linux-64::pixman-0.40.0-h7f8727e_1
xorg-fixesproto conda-forge/linux-64::xorg-fixesproto-5.0-hb9d3cd8_1003
xorg-inputproto conda-forge/linux-64::xorg-inputproto-2.3.2-hb9d3cd8_1003
xorg-kbproto conda-forge/linux-64::xorg-kbproto-1.0.7-hb9d3cd8_1003
xorg-libx11 conda-forge/linux-64::xorg-libx11-1.8.9-h8ee46fc_0
xorg-libxext conda-forge/linux-64::xorg-libxext-1.3.4-h0b41bf4_2
xorg-libxfixes conda-forge/linux-64::xorg-libxfixes-5.0.3-h7f98852_1004
xorg-libxi conda-forge/linux-64::xorg-libxi-1.7.10-h4bc722e_1
xorg-libxrender conda-forge/linux-64::xorg-libxrender-0.9.11-hd590300_0
xorg-libxtst conda-forge/linux-64::xorg-libxtst-1.2.5-h4bc722e_0
xorg-recordproto conda-forge/linux-64::xorg-recordproto-1.14.2-hb9d3cd8_1003
xorg-renderproto conda-forge/linux-64::xorg-renderproto-0.11.1-hb9d3cd8_1003
xorg-xextproto conda-forge/linux-64::xorg-xextproto-7.3.0-hb9d3cd8_1004
xorg-xproto pkgs/main/linux-64::xorg-xproto-7.0.31-h27cfd23_1007
zstd pkgs/main/linux-64::zstd-1.5.5-hc292b87_2
The following packages will be UPDATED:
gatk4 4.3.0.0-py36hdfd78af_0 --> 4.5.0.0-py36hdfd78af_0
glib 2.69.1-h4ff587b_1 --> 2.78.4-h6a678d5_0
htslib 1.17-h6bc39ce_1 --> 1.18-h81da01d_0
krb5 1.20.1-h568e23c_1 --> 1.21.3-h143b758_0
libcurl pkgs/main::libcurl-7.88.1-h91b91d3_2 --> conda-forge::libcurl-8.4.0-hca28451_0
libdeflate pkgs/main::libdeflate-1.17-h5eee18b_1 --> conda-forge::libdeflate-1.21-h4bc722e_0
libffi 3.3-he6710b0_2 --> 3.4.4-h6a678d5_1
libnghttp2 1.52.0-ha637b67_1 --> 1.57.0-h2d74bed_0
libssh2 1.10.0-h37d81fd_2 --> 1.11.0-h251f7ec_0
openjdk pkgs/main::openjdk-11.0.13-h87a67e3_0 --> conda-forge::openjdk-17.0.3-hea3dc9f_3
openssl pkgs/main::openssl-1.1.1w-h7f8727e_0 --> conda-forge::openssl-3.3.2-hb9d3cd8_0
python conda-forge::python-3.9.0-hffdb5ce_5_~ --> pkgs/main::python-3.9.19-h955ad1f_1
xz 5.2.10-h5eee18b_1 --> 5.4.6-h5eee18b_1
Proceed ([y]/n)? y
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
再次測(cè)試
celescope --help
usage: celescope [-h] [-v]
{rna,vdj,tag,dynaseq,snp,capture_virus,fusion,citeseq,flv_trust4,sweetseq,utils,bulk_vdj,bulk_rna,rna_5p3p} ...
CeleScope
positional arguments:
{rna,vdj,tag,dynaseq,snp,capture_virus,fusion,citeseq,flv_trust4,sweetseq,utils,bulk_vdj,bulk_rna,rna_5p3p}
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
安裝成功！９淇跷跪！
查看環(huán)境
conda info --envs
刪除環(huán)境
conda env remove -n celescope
參考資料：
doc/user_guide.md · Singleron-RD/CeleScope - Gitee.com
GitHub - singleron-RD/CeleScope: Single Cell Analysis Pipelines
https://cn.singleronbio.com/product/detail-28.html
