Linux软件安装
conda
删除频道用vim
$ vim ~/.condarc #然后dd删一行
实战演练：配置频道、创建小环境、安装软件
1.添加频道（北外或者清华皆可，方法1方法2任选其一即可）
2.创建名为rnaseq的小环境
3.激活rnaseq这个小环境
4.在rnaseq小环境中先安装fastqc，再一条命令安装fastp和hisat2
刚开始使用清华的频道镜像，创建rnaseq环境时很慢，就换成了北外的。直接删掉清华的，重新复制粘贴北外的就好。
image.png
http504报错，网络问题
换镜像
$ vim ~/.condarc
channels:
- https://mirrors.bfsu.edu.cn/anaconda/cloud/bioconda/
- https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge/
- https://mirrors.bfsu.edu.cn/anaconda/pkgs/main/
- https://mirrors.bfsu.edu.cn/anaconda/pkgs/free/
- defaults
show_channel_urls: true
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"~/.condarc" 7L, 268C
$ rm ~/.condarc
然后复制粘贴北外镜像
conda create -n rnaseq
课堂练习：
1.确认激活 rnaseq 小环境，使用mamba或者conda下载并安装以下软件
• sra-tools=2.10.7
• fastqc
• trim-galore
• hisat2
• subread
• multiqc
• samtools
• salmon
• fastp
2.调出所有安装的生信软件的帮助文档
尤其要注意salmon和fastp这两个软件
$ conda activate rnaseq
(rnaseq) Last2 09:43:33 ~
$ mamba install sra-tools=2.10.7 fastqc trim-galore hisat2 subread multiqc samtools salmon fastp
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (0.7.8) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['sra-tools=2.10.7', 'fastqc', 'trim-galore', 'hisat2', 'subread', 'multiqc', 'samtools', 'salmon', 'fastp']
anaconda/cloud/bioconda/ [====================] (00m:03s) Done
anaconda/cloud/bioconda/ [====================] (00m:05s) Done
pkgs/r/linux-64 [====================] (00m:00s) No change
anaconda/pkgs/main/noarc [====================] (00m:00s) Done
pkgs/r/noarch [====================] (00m:00s) No change
anaconda/cloud/conda-for [====================] (00m:08s) Done
anaconda/pkgs/free/noarc [====================] (00m:00s) No change
anaconda/pkgs/free/linux [====================] (00m:00s) No change
pkgs/main/noarch [====================] (00m:03s) Done
anaconda/cloud/conda-for [====================] (00m:15s) Done
anaconda/pkgs/main/linux [====================] (00m:21s) Done
pkgs/main/linux-64 [====================] (01m:53s) Done
Encountered problems while solving.
Problem: package trim-galore-0.4.1-0 requires cutadapt, but none of the providers can be installed
(rnaseq) Last2 09:50:36 ~
安装的时候使用了r,main这些频道，不出错不管，出错比如卡住，就删掉defaults.
$ vim ~/.condarc
dd
(rnaseq) Last2 10:03:23 ~
提示信息trim-galore-0.4.1-0 requires cutadapt，trim-galore并没有装成功
试过单独安装trim-galore，在anconda上找安装代码运行，结果都是同样的报错
换个思路，先手动装上cutadapt
$ mamba install cutadapt
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (0.7.8) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['cutadapt']
anaconda/cloud/bioconda/ [====================] (00m:00s) No change
anaconda/cloud/bioconda/ [====================] (00m:00s) No change
anaconda/cloud/conda-for [====================] (00m:00s) No change
anaconda/cloud/conda-for [====================] (00m:00s) No change
anaconda/pkgs/main/linux [====================] (00m:00s) No change
anaconda/pkgs/free/noarc [====================] (00m:00s) No change
anaconda/pkgs/free/linux [====================] (00m:00s) No change
anaconda/pkgs/main/noarc [====================] (00m:00s) No change
Encountered problems while solving.
Problem: package cutadapt-2.10-py38h0213d0e_1 requires python >=3.8,<3.9.0a0, but none of the providers can be installed
(rnaseq) Last2 10:26:58 ~
发现是cutadapt依赖的python版本出问题，导致cutadapt装不上，cutadapt装不上又导致trim-galore装不上
$ mamba list
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (0.7.8) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
# packages in environment at /trainee1/Last2/miniconda3/envs/rnaseq:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
_openmp_mutex 4.5 1_gnu https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
alsa-lib 1.2.3 h516909a_0 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
ca-certificates 2020.12.5 ha878542_0 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
cairo 1.16.0 h7979940_1007 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
certifi 2020.12.5 py39hf3d152e_1 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
fastp 0.20.1 h8b12597_0 https://mirrors.bfsu.edu.cn/anaconda/cloud/bioconda
fastqc 0.11.9 0 https://mirrors.bfsu.edu.cn/anaconda/cloud/bioconda
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
fontconfig 2.13.1 hba837de_1004 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
freetype 2.10.4 h0708190_1 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
gettext 0.19.8.1 h0b5b191_1005 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
giflib 5.2.1 h516909a_2 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
graphite2 1.3.14 h23475e2_0 https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
harfbuzz 2.7.4 h5cf4720_0 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
hisat2 2.2.1 he1b5a44_2 https://mirrors.bfsu.edu.cn/anaconda/cloud/bioconda
icu 68.1 h58526e2_0 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
jpeg 9d h516909a_0 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
lcms2 2.11 hcbb858e_1 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
ld_impl_linux-64 2.35.1 hea4e1c9_1 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
libffi 3.3 h58526e2_2 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
libgcc-ng 9.3.0 h2828fa1_18 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
libglib 2.66.4 hf9edacf_1 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
libgomp 9.3.0 h2828fa1_18 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
libiconv 1.16 h516909a_0 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
libpng 1.6.37 hed695b0_2 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
libstdcxx-ng 9.3.0 h6de172a_18 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
libtiff 4.2.0 hdc55705_0 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
libuuid 2.32.1 h14c3975_1000 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
libwebp-base 1.1.0 h516909a_3 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
libxcb 1.14 h7b6447c_0 https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
libxml2 2.9.10 h72842e0_3 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
lz4-c 1.9.3 h9c3ff4c_0 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
ncurses 6.2 h58526e2_4 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
openjdk 11.0.8 hacce0ff_0 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
openssl 1.1.1i h7f98852_0 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
pcre 8.44 he1b5a44_0 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
perl 5.32.0 h36c2ea0_0 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
pip 20.3.3 pyhd8ed1ab_0 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
pixman 0.40.0 h36c2ea0_0 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
python 3.9.1 hffdb5ce_3_cpython https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge #现在的python版本3.9.1
python_abi 3.9 1_cp39 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
readline 8.0 he28a2e2_2 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
setuptools 49.6.0 py39hf3d152e_3 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
sqlite 3.34.0 h74cdb3f_0 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
tk 8.6.10 h21135ba_1 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
tzdata 2020f he74cb21_0 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
wheel 0.36.2 pyhd3deb0d_0 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
xorg-fixesproto 5.0 h14c3975_1002 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
xorg-inputproto 2.3.2 h14c3975_1002 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
xorg-kbproto 1.0.7 h14c3975_1002 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
xorg-libice 1.0.10 h516909a_0 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
xorg-libsm 1.2.3 h84519dc_1000 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
xorg-libx11 1.6.12 h516909a_0 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
xorg-libxext 1.3.4 h516909a_0 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
xorg-libxfixes 5.0.3 h516909a_1004 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
xorg-libxi 1.7.10 h516909a_0 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
xorg-libxrender 0.9.10 h516909a_1002 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
xorg-libxtst 1.2.3 h516909a_1002 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
xorg-recordproto 1.14.2 h516909a_1002 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
xorg-renderproto 0.11.1 h14c3975_1002 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
xorg-xextproto 7.3.0 h14c3975_1002 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
xorg-xproto 7.0.31 h14c3975_1007 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
xz 5.2.5 h516909a_1 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
zlib 1.2.11 h516909a_1010 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
zstd 1.4.8 ha95c52a_1 https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
(rnaseq) Last2 10:32:06 ~
$ mamba install python=3.8
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (0.7.8) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['python=3.8']
anaconda/cloud/bioconda/ [====================] (00m:00s) No change
anaconda/cloud/bioconda/ [====================] (00m:00s) No change
anaconda/cloud/conda-for [====================] (00m:00s) No change
anaconda/cloud/conda-for [====================] (00m:00s) No change
anaconda/pkgs/main/linux [====================] (00m:00s) No change
anaconda/pkgs/free/noarc [====================] (00m:00s) No change
anaconda/pkgs/free/linux [====================] (00m:00s) No change
anaconda/pkgs/main/noarc [====================] (00m:00s) No change
Transaction
Prefix: /trainee1/Last2/miniconda3/envs/rnaseq
Updating specs:
- python==3.8
Package Version Build Channel Size
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Change:
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
certifi 2020.12.5 py39hf3d152e_1 installed
certifi 2020.12.5 py38h578d9bd_1 mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge/linux-64 Cached
Upgrade:
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
ca-certificates 2020.12.5 ha878542_0 installed
ca-certificates 2021.1.19 h06a4308_0 mirrors.bfsu.edu.cn/anaconda/pkgs/main/linux-64 121 KB
setuptools 49.6.0 py39hf3d152e_3 installed
setuptools 51.3.3 py38h06a4308_4 mirrors.bfsu.edu.cn/anaconda/pkgs/main/linux-64 727 KB
Downgrade:
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
python 3.9.1 hffdb5ce_3_cpython installed
python 3.8.6 hffdb5ce_4_cpython mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge/linux-64 26 MB
python_abi 3.9 1_cp39 installed
python_abi 3.8 1_cp38 mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge/linux-64 Cached
Summary:
Change: 1 packages
Upgrade: 2 packages
Downgrade: 2 packages
Total download: 27 MB
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n] y
Finished ca-certificates (00m:00s) 121 KB 473 KB/s
Finished setuptools (00m:00s) 727 KB 2 MB/s
Finished python (00m:05s) 26 MB 18 MB/s
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(rnaseq) Last2 10:39:20 ~
$ mamba install trim-galore
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (0.7.8) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['trim-galore']
anaconda/cloud/bioconda/ [====================] (00m:00s) No change
anaconda/cloud/conda-for [====================] (00m:00s) No change
anaconda/cloud/conda-for [====================] (00m:00s) No change
anaconda/pkgs/main/linux [====================] (00m:00s) No change
anaconda/cloud/bioconda/ [====================] (00m:00s) No change
anaconda/pkgs/free/noarc [====================] (00m:00s) No change
anaconda/pkgs/free/linux [====================] (00m:00s) No change
anaconda/pkgs/main/noarc [====================] (00m:00s) No change
Transaction
Prefix: /trainee1/Last2/miniconda3/envs/rnaseq
Updating specs:
- trim-galore
Package Version Build Channel Size
────────────────────────────────────────────────────────────────────────────────────────────────────────────
Install:
────────────────────────────────────────────────────────────────────────────────────────────────────────────
cutadapt 3.2 py38h0213d0e_0 mirrors.bfsu.edu.cn/anaconda/cloud/bioconda/linux-64 191 KB
dnaio 0.5.0 py38h0213d0e_0 mirrors.bfsu.edu.cn/anaconda/cloud/bioconda/linux-64 130 KB
isa-l 2.30.0 h7f98852_1 mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge/linux-64 295 KB
pigz 2.4 h84994c4_0 mirrors.bfsu.edu.cn/anaconda/pkgs/main/linux-64 64 KB
python-isal 0.3.0 py38h497a2fe_0 mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge/linux-64 100 KB
trim-galore 0.6.6 0 mirrors.bfsu.edu.cn/anaconda/cloud/bioconda/noarch 42 KB
xopen 1.1.0 py38h578d9bd_0 mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge/linux-64 20 KB
Summary:
Install: 7 packages
Total download: 842 KB
────────────────────────────────────────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n] y
Finished pigz (00m:00s) 64 KB 294 KB/s
Finished python-isal (00m:00s) 100 KB 287 KB/s
Finished xopen (00m:00s) 20 KB 55 KB/s
Finished trim-galore (00m:00s) 42 KB 104 KB/s
Finished dnaio (00m:00s) 130 KB 308 KB/s
Finished cutadapt (00m:00s) 191 KB 449 KB/s
Finished isa-l (00m:00s) 295 KB 660 KB/s
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(rnaseq) Last2 10:44:59 ~
发现跟安装软件的顺序有关，这样就不会报错
image.png
误区：装什么软件就调用什么软件是不对的，装的可能是个软件包或子程序的集合
python版本降低，有可能其他软件用不了。所以用help来试。安装成功出现三个done + 成功调取这个软件的帮助文档=软件安装成功
分清软件名和命令名
sra-tools是一个软件包，真正使用的是prefetch。因为sra-tools是软件包的名字，我们后面要调用的是这个软件包里面的prefetch之类的子程序，所以测试一下prefetch或者fastq-dump的帮助文档能否调用即可。这个sratools就不是通过-h之类的方式调用帮助文档的。如果是打错了，它报的错应该是command not found。
subread是软件名，用featureCounts
$ prefetch -h
Usage: prefetch [ options ] [ accessions(s)... ]
Parameters:
accessions(s) list of accessions to process
Options:
-T|--type Specify file type to download. Default: sra
-N|--min-size Minimum file size to download in KB
(inclusive).
-X|--max-size Maximum file size to download in KB
(exclusive). Default: 20G
-f|--force Force object download - one of: no, yes,
all, ALL. no [default]: skip download if
the object if found and complete; yes:
download it even if it is found and is
complete; all: ignore lock files (stale
locks or it is being downloaded by
another process - use at your own
risk!); ALL: ignore lock files, restart
download from beginning
-p|--progress Show progress
-r|--resume Resume partial downloads - one of: no, yes
[default]
-C|--verify Verify after download - one of: no, yes
[default]
-c|--check-all Double-check all refseqs
-o|--output-file Write file to when downloading
single file
-O|--output-directory
Save files to /
--ngc to ngc file
--perm to permission file
--location location in cloud
--cart to cart file
--disable-multithreading disable multithreading
-V|--version Display the version of the program
-L|--log-level Logging level as number or enum string.
One of
(fatal|sys|int|err|warn|info|debug) or
(0-6) Current/default is warn
--option-file file Read more options and parameters from the
file.
-h|--help print this message
"prefetch" version 2.10.7
(rnaseq) Last2 11:05:29 ~
$ fastqc -h
FastQC - A high throughput sequence QC analysis tool
SYNOPSIS
fastqc seqfile1 seqfile2 .. seqfileN
fastqc [-o output dir] [--(no)extract] [-f fastq|bam|sam]
[-c contaminant file] seqfile1 .. seqfileN
DESCRIPTION
FastQC reads a set of sequence files and produces from each one a quality
control report consisting of a number of different modules, each one of
which will help to identify a different potential type of problem in your
data.
If no files to process are specified on the command line then the program
will start as an interactive graphical application. If files are provided
on the command line then the program will run with no user interaction
required. In this mode it is suitable for inclusion into a standardised
analysis pipeline.
The options for the program as as follows:
-h --help Print this help file and exit
-v --version Print the version of the program and exit
-o --outdir Create all output files in the specified output directory.
Please note that this directory must exist as the program
will not create it. If this option is not set then the
output file for each sequence file is created in the same
directory as the sequence file which was processed.
--casava Files come from raw casava output. Files in the same sample
group (differing only by the group number) will be analysed
as a set rather than individually. Sequences with the filter
flag set in the header will be excluded from the analysis.
Files must have the same names given to them by casava
(including being gzipped and ending with .gz) otherwise they
won't be grouped together correctly.
--nano Files come from nanopore sequences and are in fast5 format. In
this mode you can pass in directories to process and the program
will take in all fast5 files within those directories and produce
a single output file from the sequences found in all files.
--nofilter If running with --casava then don't remove read flagged by
casava as poor quality when performing the QC analysis.
--extract If set then the zipped output file will be uncompressed in
the same directory after it has been created. By default
this option will be set if fastqc is run in non-interactive
mode.
-j --java Provides the full path to the java binary you want to use to
launch fastqc. If not supplied then java is assumed to be in
your path.
--noextract Do not uncompress the output file after creating it. You
should set this option if you do not wish to uncompress
the output when running in non-interactive mode.
--nogroup Disable grouping of bases for reads >50bp. All reports will
show data for every base in the read. WARNING: Using this
option will cause fastqc to crash and burn if you use it on
really long reads, and your plots may end up a ridiculous size.
You have been warned!
--min_length Sets an artificial lower limit on the length of the sequence
to be shown in the report. As long as you set this to a value
greater or equal to your longest read length then this will be
the sequence length used to create your read groups. This can
be useful for making directly comaparable statistics from
datasets with somewhat variable read lengths.
-f --format Bypasses the normal sequence file format detection and
forces the program to use the specified format. Valid
formats are bam,sam,bam_mapped,sam_mapped and fastq
-t --threads Specifies the number of files which can be processed
simultaneously. Each thread will be allocated 250MB of
memory so you shouldn't run more threads than your
available memory will cope with, and not more than
6 threads on a 32 bit machine
-c Specifies a non-default file which contains the list of
--contaminants contaminants to screen overrepresented sequences against.
The file must contain sets of named contaminants in the
form name[tab]sequence. Lines prefixed with a hash will
be ignored.
-a Specifies a non-default file which contains the list of
--adapters adapter sequences which will be explicity searched against
the library. The file must contain sets of named adapters
in the form name[tab]sequence. Lines prefixed with a hash
will be ignored.
-l Specifies a non-default file which contains a set of criteria
--limits which will be used to determine the warn/error limits for the
various modules. This file can also be used to selectively
remove some modules from the output all together. The format
needs to mirror the default limits.txt file found in the
Configuration folder.
-k --kmers Specifies the length of Kmer to look for in the Kmer content
module. Specified Kmer length must be between 2 and 10. Default
length is 7 if not specified.
-q --quiet Supress all progress messages on stdout and only report errors.
-d --dir Selects a directory to be used for temporary files written when
generating report images. Defaults to system temp directory if
not specified.
BUGS
Any bugs in fastqc should be reported either to [email protected]
or in www.bioinformatics.babraham.ac.uk/bugzilla/
(rnaseq) Last2 11:05:56 ~
trim-galore --help不行，用trim_galore
$ trim-galore --help
trim-galore: command not found
(rnaseq) Last2 11:07:35 ~
$ trim_galore --help
USAGE:
trim_galore [options]
-h/--help Print this help message and exits.
-v/--version Print the version information and exits.
-q/--quality Trim low-quality ends from reads in addition to adapter removal. For
RRBS samples, quality trimming will be performed first, and adapter
trimming is carried in a second round. Other files are quality and adapter
trimmed in a single pass. The algorithm is the same as the one used by BWA
(Subtract INT from all qualities; compute partial sums from all indices
to the end of the sequence; cut sequence at the index at which the sum is
minimal). Default Phred score: 20.
$ hisat2 -h
HISAT2 version 2.2.1 by Daehwan Kim ([email protected], www.ccb.jhu.edu/people/infphilo)
Usage:
hisat2 [options]* -x {-1 -2 | -U } [-S ]
Index filename prefix (minus trailing .X.ht2).
Files with #1 mates, paired with files in .
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
Files with #2 mates, paired with files in .
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
Files with unpaired reads.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
File for SAM output (default: stdout)
, , can be comma-separated lists (no whitespace) and can be
specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'.
Options (defaults in parentheses):
Input:
-q query input files are FASTQ .fq/.fastq (default)
--qseq query input files are in Illumina's qseq format
-f query input files are (multi-)FASTA .fa/.mfa
subread用featureCounts -h
$ featureCounts -h
featureCounts: invalid option -- 'h'
Version 2.0.1
Usage: featureCounts [options] -a -o input_file1 [input_file2] ...
## Mandatory arguments:
-a Name of an annotation file. GTF/GFF format by default. See
-F option for more format information. Inbuilt annotations
(SAF format) is available in 'annotation' directory of the
package. Gzipped file is also accepted.
$ multiqc -h
Usage: multiqc [OPTIONS]
Main MultiQC run command for use with the click command line, complete
with all click function decorators. To make it easy to use MultiQC within
notebooks and other locations that don't need click, we simply pass the
parsed variables on to a vanilla python function.
Options:
-f, --force Overwrite any existing reports
-d, --dirs Prepend directory to sample names
-dd, --dirs-depth INTEGER Prepend [INT] directories to sample names.
Negative number to take from start of path.
$ samtools
Program: samtools (Tools for alignments in the SAM format)
Version: 1.11 (using htslib 1.11)
Usage: samtools [options]
Commands:
-- Indexing
dict create a sequence dictionary file
faidx index/extract FASTA
fqidx index/extract FASTQ
index index alignment
-- Editing
calmd recalculate MD/NM tags and '=' bases
fixmate fix mate information
reheader replace BAM header
targetcut cut fosmid regions (for fosmid pool only)
addreplacerg adds or replaces RG tags
markdup mark duplicates
ampliconclip clip oligos from the end of reads
$ salmon
salmon v1.4.0
Usage: salmon -h|--help or
salmon -v|--version or
salmon -c|--cite or
salmon [--no-version-check] [-h | options]
Commands:
index : create a salmon index
quant : quantify a sample
alevin : single cell analysis
swim : perform super-secret operation
quantmerge : merge multiple quantifications into a single file
(rnaseq) Last2 12:01:07 ~
$ fastp
fastp: an ultra-fast all-in-one FASTQ preprocessor
version 0.20.1
usage: fastp [options] ...
options:
-i, --in1 read1 input file name (string [=])
-o, --out1 read1 output file name (string [=])
-I, --in2 read2 input file name (string [=])
-O, --out2 read2 output file name (string [=])
--unpaired1 for PE input, if read1 passed QC but read2 not, it will be written to unpaired1. Default is to discard it. (string [=])
--unpaired2 for PE input, if read2 passed QC but read1 not, it will be written to unpaired2. If --unpaired2 is same as --unpaired1 (default mode), both unpaired reads will be written to this same file. (string [=])
--failed_out specify the file to store reads that cannot pass the filters. (string [=])
环境变量
加引号或不加引号都是原模原样输出
$ echo '123'
123
(rnaseq) Last2 12:23:18 ~
$ echo 123
123
(rnaseq) Last2 12:23:24 ~
不可以空格，会被当成命令
$ a = 10 #不可以空格，会被当成命令
a: command not found
(rnaseq) Last2 12:21:17 ~
$ a=10
(rnaseq) Last2 12:21:24 ~
$ echo a
a
(rnaseq) Last2 12:21:29 ~
$ echo $a
10
(rnaseq) Last2 12:21:39 ~