可以使用conda 安装sickle
(rna) $ conda install sickle
Retrieving notices: ...working... done
Channels:
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
- defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done
## Package Plan ##
added / updated specs:
- sickle
The following packages will be downloaded:
package | build
---------------------------|-----------------
libxslt-1.1.35 | h4e12654_0 453 KB defaults
lxml-4.5.0 | py27hcde611f_1 1.5 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
sickle-0.7.0 | pyh9f0ad1d_0 15 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
------------------------------------------------------------
Total: 2.0 MB
The following NEW packages will be INSTALLED:
libxslt anaconda/pkgs/main/linux-64::libxslt-1.1.35-h4e12654_0
lxml anaconda/cloud/conda-forge/linux-64::lxml-4.5.0-py27hcde611f_1
sickle anaconda/cloud/bioconda/noarch::sickle-0.7.0-pyh9f0ad1d_0
Proceed ([y]/n)? y
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
但是无法使用，也有人有一样的问题
sickle not found though installed. · Issue #58 · najoshi/sickle (github.com)
(rna) $ sickle pe
-bash: sickle: command not found
(rna) $ which sickle
(rna) $ conda list|grep sickle
sickle 0.7.0 pyh9f0ad1d_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
有教程提到应该安装 sickletrim
3. Quality control (sschmeier.com)
(rna) $ conda install sickle-trim
Channels:
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
- defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done
## Package Plan ##
added / updated specs:
- sickle-trim
The following packages will be downloaded:
package | build
---------------------------|-----------------
sickle-trim-1.33 | he4a0461_9 21 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
------------------------------------------------------------
Total: 21 KB
The following NEW packages will be INSTALLED:
sickle-trim anaconda/cloud/bioconda/linux-64::sickle-trim-1.33-he4a0461_9
Proceed ([y]/n)? y
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(rna)$ sickle -h
Usage: sickle <command> [options]
Command:
pe paired-end sequence trimming
se single-end sequence trimming
--help, display this help and exit
--version, output version information and exit
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