doctor.py 初接触

这次想好了好好学习,下来血本,按照推荐配了一台个人的服务器。这周刚刚点亮。工作站主机E5-2683 V3正式版CPU28核56线程双路E5服务器。

主板:超微X10DAI

CPU: E5-2683 V3  x2

内存:三星 REG DDR4 16G

硬盘:2T 机械硬盘

亮卡机:GT 610 淘宝二手65元包邮

组装好后,快递回来的。这部分的费用是10200+65¥的费用。。。

回来买了一台27寸的三星显示器 1599¥,买了VGI的连接线35。。。

借着下班回来的的短暂时间,试了机器感觉还是很不错。回来点亮了机器,诧异的是插上网线,并未填写过密码,电脑直接就可以联网了。一起下来12000¥。刚刚开始还是不习惯linux的系统。不停地在笔记本上和台式的linux系统上不停地切换。

按照Bio-star上的说明。运行了doctor.py.

最开始的15个13个显示error。反复倒腾过后开始慢慢了解怎么安装转件。现在还在9个error。其实家里的网也不慢,发现linux的下载速度都是超级慢,再装hisat2时,只有32M,却下载了整整80min。简直罪过了。以前只知道找分析的人要什么样的图,现在发现大家都不容易。干分析和做实验还是很像的,都有一个protocol,一步一步慢慢走才行。目前我按还是照生信媛的biostar课程慢慢开始吧。

admin1@hyl:~$ mkdir -p ~/bin

admin1@hyl:~$ curl http://data.biostarhandbook.com/install/doctor.py>~/bin/doctor.py

% Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

Dload  Upload   Total   Spent    Left  Speed

100  3570  100  3570    0     0    976      0  0:00:03  0:00:03 --:--:--   976

admin1@hyl:~$ chmod +x ~/bin/doctor.py

admin1@hyl:~$  ~/bin/doctor.py

# Doctor! Doctor! Give me the news.

# The ~/bin folder is not in your PATH!

# Checking 15 symptoms...

# Missing program: bwa

# Missing program: datamash

# Missing program: fastqc

# Missing program: hisat2

# Missing program: seqret

# Missing program: subread-align

# Missing program: featureCounts

# Missing program: R

# Missing program: efetch

# Missing program: esearch

# Missing program: samtools

# Missing program: fastq-dump

# Optional program not found: wonderdump

# Optional program not found: global-align.sh

# Optional program not found: local-align.sh

# Your system shows 13 errors.

# See also: doctor.py --fixme

admin1@hyl:~$ PATH=$PATH:~/bin

admin1@hyl:~$ doctor.py --fixme

cd ~/biosoft

mkdir HISAT&&cd HISAT

wget ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.0.4-Linux_x86_64.zip

unzip hisat2-2.0.4-Linux_x86_64.zip

ln -s hisat2-2.0.4  current

cd ~/biosoft

mkdir HTSeq&&cd HTSeq

wget  https://pypi.python.org/packages/72/0f/566afae6c149762af301a19686cd5fd1876deb2b48d09546dbd5caebbb78/HTSeq-0.6.1.tar.gz

tar zxvf HTSeq-0.6.1.tar.gz

cd HTSeq-0.6.1

python setup.py install --user

~/.local/bin/htseq-count  --help

admin1@hyl:~$ doctor.py

# Doctor! Doctor! Give me the news.

# Checking 15 symptoms...

# Missing program: bwa

# Missing program: datamash

# Missing program: fastqc

# Missing program: hisat2

# Missing program: seqret

# Missing program: subread-align

# Missing program: featureCounts

# Missing program: samtools

# Missing program: fastq-dump

# Optional program not found: wonderdump

# Optional program not found: global-align.sh

# Optional program not found: local-align.sh

# Your system shows 9 errors.

# See also: doctor.py --fixme

admin1@hyl:~$ doctor.py --fixme

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