fluff 是一个软件包，它允许对映射到参考基因组的高通量测序实验进行简单的探索、聚类和可视化。这个包包含三个命令行工具，用于生成发布质量数据
官网：https://fluff.readthedocs.io/en/latest/introduction.html
- 环境：Ubuntu 20.04 LTS，这个软件好像不支持 win？
这个安装好无语。大家的 PC 都装不上，部分机房电脑是可以装上的
但是既然决定 PC 上用 Ubuntu 了，那就要贯彻到底了
# 方法
# 官方最简安装方法：用 conda 安装
conda config --add channels defaults | |
conda config --add channels conda-forge | |
conda config --add channels bioconda | |
conda install biofluff -c bioconda |
但是这个方法。得安一小时，还报错。一开始以为是机房网不好，后来网好了发现也那么慢，唔，那没事了，可能是因为直接从外国服务器上下载的吧
# 第二种方法：用 pip
pip install biofluff |
这个还挺快的，但有报错
Building wheel for pyBigWig (setup.py) ... error | |
...... | |
Running setup.py install for pyBigWig ... error |
少 pyBigWig 这个包
# 比较麻烦的方法：源码安装
可以全部用命令行，用 git
git clone https://github.com/simonvh/fluff.git | |
cd fluff |
也可以图形界面浏览器直接到 https://github.com/simonvh/fluff/releases 下载压缩包
最新的版本是 3.0.3
cd /opt | |
sudo mkdir fluff | |
# 去 /opt 目录下创建 fluff 的文件夹 | |
sudo tar xvzf fluff-3.0.3.tar.gz -C /opt/fluff | |
# 解压到 /opt/fluff 目录下 | |
cd /opt/fluff/fluff-3.0.3 |
编译
sudo python setup.py build |
报错
sudo: python：找不到命令 |
这个可能是 anaconda 和自带 python 冲突了？反正是没有在 bin 里关联全局指令
用 which 命令看 python 的位置
which python | |
# 返回 /home/limin/anaconda3/bin/python | |
# 那就这么写 | |
sudo /home/limin/anaconda3/bin/python setup.py build | |
sudo /home/limin/anaconda3/bin/python setup.py install |
报错
Either libcurl isn't installed, it didn't come with curl-config, or curl-config isn't in your $PATH. pyBigWig will be installed without support for remote files. | |
...... | |
No eggs found in /tmp/easy_install-b42ki6n5/pyBigWig-0.3.17/egg-dist-tmp-syp78d48 (setup script problem?) | |
error: The 'pyBigWig' distribution was not found and is required by biofluff |
大概还是少 pyBigWig 这个包，而且这个包依赖
再来一遍 还是报错
Installed /home/limin/anaconda3/lib/python3.8/site-packages/biofluff-3.0.3-py3.8.egg | |
Processing dependencies for biofluff==3.0.3 | |
Searching for pyBigWig | |
Reading https://pypi.org/simple/pyBigWig/ | |
Download error on https://pypi.org/simple/pyBigWig/: [Errno -3] Temporary failure in name resolution -- Some packages may not be found! | |
Couldn't find index page for 'pyBigWig' (maybe misspelled?) | |
Scanning index of all packages (this may take a while) | |
Reading https://pypi.org/simple/ | |
Download error on https://pypi.org/simple/: [Errno -3] Temporary failure in name resolution -- Some packages may not be found! | |
No local packages or working download links found for pyBigWig | |
error: Could not find suitable distribution for Requirement.parse('pyBigWig') |
# 解决
第一种方法不要了
从后两种方法的报错来看，主要问题：缺少 pyBigWig
装就完了
sudo pip install pyBigWig==0.2.5 |
报错
sudo: pip：找不到命令 |
真烦人。去 conda 里装
conda activate | |
pip install pyBigWig==0.2.5 |
报错
In file included from libBigWig/bigWig.h:1, | |
from libBigWig/bwStats.c:1: | |
libBigWig/io.h:1:10: fatal error: curl/curl.h: 没有那个文件或目录 | |
1 #include | |
^~~~~~~~~~~~~ | |
compilation terminated. | |
error: command 'gcc' failed with exit status 1 | |
---------------------------------------- | |
ERROR: Failed building wheel for pyBigWig |
少 curl 依赖，装
sudo apt-get install curl libcurl4 libcurl4-openssl-dev |
再装 pyBigWig 就可以了
pip install pyBigWig==0.2.5 |
成功后再装 biofluff
pip install biofluff |
成功了！运行 fluff
(base) limin@limin-Lenovo-XiaoXin-Air-15IKBR:~$ fluff | |
/home/limin/anaconda3/lib/python3.8/site-packages/biofluff-3.0.3-py3.8.egg/fluff/track.py:46: SyntaxWarning: "is not" with a literal. Did you mean "!="? | |
/home/limin/anaconda3/lib/python3.8/site-packages/biofluff-3.0.3-py3.8.egg/fluff/track.py:46: SyntaxWarning: "is" with a literal. Did you mean "=="? | |
/home/limin/anaconda3/lib/python3.8/site-packages/biofluff-3.0.3-py3.8.egg/fluff/track.py:51: SyntaxWarning: "is not" with a literal. Did you mean "!="? | |
/home/limin/anaconda3/lib/python3.8/site-packages/biofluff-3.0.3-py3.8.egg/fluff/track.py:51: SyntaxWarning: "is" with a literal. Did you mean "=="? | |
/home/limin/anaconda3/lib/python3.8/site-packages/biofluff-3.0.3-py3.8.egg/fluff/track.py:46: SyntaxWarning: "is not" with a literal. Did you mean "!="? | |
/home/limin/anaconda3/lib/python3.8/site-packages/biofluff-3.0.3-py3.8.egg/fluff/track.py:46: SyntaxWarning: "is" with a literal. Did you mean "=="? | |
/home/limin/anaconda3/lib/python3.8/site-packages/biofluff-3.0.3-py3.8.egg/fluff/track.py:51: SyntaxWarning: "is not" with a literal. Did you mean "!="? | |
/home/limin/anaconda3/lib/python3.8/site-packages/biofluff-3.0.3-py3.8.egg/fluff/track.py:51: SyntaxWarning: "is" with a literal. Did you mean "=="? | |
usage: fluff [-h] [options] | |
fluff v3.0.3 | |
positional arguments: | |
{heatmap,bandplot,profile} | |
optional arguments: | |
-h, --help show this help message and exit | |
commands: | |
heatmap Produce a heatmap | |
bandplot Show the profiles as bandplots | |
profile Genome Browser screenshot | |
type </span>fluff <span class="token operator"><</span>command<span class="token operator">></span> -h<span class="token variable"> for more details |
有一点报错，但是不影响使用。
