cloud cmd install

 

 

 

Install

The installation of file manager is very simple.

  • install latest version of node.js.
  • install cloudcmd via npm with:
npm i cloudcmd -g

When in trouble use:

npm i cloudcmd -g --force

sudo vi /usr/lib/node_modules/cloudcmd/json/config.json

“dirStorage”: false,
“online”: true,
“open”: false,
“keysPanel”: true,
“port”: 8080,
“ip”: “143.89.31.17”,
“root”: “/”,
“prefix”: “”,
“progress”: true,
“contact”: true,
“confirmCopy”: true,
“confirmMove”: true,
“configDialog”: true,
“oneFilePanel”: false,
“console”: true,
“syncC[……]

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Basic Usage of tmap

import sklearn

import plotly.plotly as py
import plotly.graph_objs as go

import matplotlib.pyplot as plt
import numpy as np

from sklearn.cluster import DBSCAN
from sklearn import metrics
from sklearn.datasets.samples_generator import make_blobs
from sklearn.preprocessing import StandardScaler




###################################
# Load libraries
from sklearn import datasets
from sklearn.preprocessing import StandardScaler
from sklearn.cluster import DBSCAN
from sklearn.preprocessing import MinMaxScaler

###################################



shenzy@SZYENVS:~/[......]

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Good measure to download sequence from NCBI based on acc or gi number

cat file_with_ids.txt | while read p; do echo $p; esearch -db nucleotide -query $p | efetch -format fasta > $p.fasta; done;

 

 

cat ginumber.txt| while read p; do echo $p; efetch -db nucleotide -id $p -format gb > $p.gbk; done;

 

shenzy@SZYENVS:~/work/zhongshan/virus_database$ cat ginumber.txt| while read p; do echo $p; efetch -db nucleotide -id $p -format gb > $p.gbk; done;
AY180661
AY180662
AY180663
AY180664
AY180665
AY180666
AY180667
AY180668
AY180669
AY180670
AY180671
AY180672
AY180673
AY180674
AY180675
AY180676
AY180677

VOSEQ server start

####

[shenzy@LFE0530 VoSeq-2.1.1]$ source /usr/bin/virtualenvwrapper.sh
[shenzy@LFE0530 VoSeq-2.1.1]$ workon voseq_environment
(voseq_environment) [shenzy@LFE0530 VoSeq-2.1.1]$

python voseq/manage.py runserver –settings=voseq.settings.local 143.89.29.80:8000

 

setup environmental variables, virtual environments

Wai-Yin Kwan edited this page on Jul 5, 2015 · 12 revisions

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Sci-Hub 最新可用网址

Pubmedy:显示影响因子+引用数、Sci-hub全文下载的浏览器扩展

很多人都知道一个下载文献的好地方 Sci-Hub,但是现在 Sci-Hub 的站长 Alexandra Elbakyan 女士面临着爱思唯尔的诉讼,让其面临数百万美元的赔偿。因此现在 Sci-Hub 在某些时候可能不可用了。不过 Alexandra Elbakyan 女士并未妥协,希望大家能多支持一下这位女士(貌似只能接受比特币捐款,我也不知道怎么弄,要是paypal或者payoneer就好了)。

相信很多人都知道下面这两个网址:

Sci-Hub 官网:http://www.sci-hub.org/

Sci-Hub 替代网址:http://www.sci-hub.io/

http://sci-hub.ac/和http://sci-hub.cc/也都已经阵亡(2017月12月6日测试)

以上几个网址都挂了,现在可用的是

http://sci-hub.bz/(12月8日测试 已经不可用了)

http://sci-hub.la/

http://sci-hub.hk/

http://sci-hub.tw/

http://sci-hub.tv/

http://80.82.77.83/

http://80.82.77.84/

fasta2nexus by R script

Workspace loaded from ~/.RData]

> setwd("/home/shenzy/work/beast/51samples")
> library(seqinr)
> data=read.fasta("51strain_core_gene_alignment.aln")
> library(ape)

Attaching package: ‘ape’

The following objects are masked from ‘package:seqinr’:

    as.alignment, consensus

> write.nexus.data(data,file="51strain_core_gene_alignment.aln.nexus", format="DNA")
>

change the font size of leaf nodes when generating phylogenetic trees using Bio.Phylo.draw()

axes : matplotlib/pylab axes If a valid matplotlib.axes.Axes instance, the phylogram is plotted in that Axes. By default (None), a new figure is created.

This means that you can load your own axes with your size of choice. For example

import matplotlib
import matplotlib.pyplot as plt
from Bio import Phylo
from cStringIO import StringIO

def plot_tree(treedata, output_file):
    handle = StringIO(treedata)  # parse the newick string
    tree = Phylo.read(handle, "newick")
    matplotlib.rc('font', size=6)
    # set the size of the figure
    fig = plt.figure(figsize=(10, 20), dpi=10[......]

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How to find large files with size in Linux? find and du command example

One of the common problem while working in UNIX is to find large files to free some space. Suppose, your file system is full and you are receiving an alert to remove spaces or if your host is run out of space and your server is not starting up, the first thing you do is find top 10 largest files and see if you can delete them. Usually, old files, large Java heap dumb are good candidates for removal and freeing up some space. If you are running Java application e.g. core java based programs or web application running on Tomcat then you can remove those heap dump files and free some space, but t[……]

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y叔的ChIP-seq数据分析大礼包(转贴)

熟悉我们生信技能树团队的应该都知道大名鼎鼎的y叔啦,作为我们论坛的荣誉顾问,y叔一直勤勤恳恳的指出我们的错误,特意在此谢谢y叔!并奉上y叔的ChIP-seq数据分析大礼包,已经征得y叔同意啦!

关注Y叔微信公众账号biobabble

CS0: ChIPseq从入门到放弃

接下来要出一个ChIPseq系列,讲一讲ChIPseq和我的ChIPseeker,从入门到放弃是我自己的个人写照。我做ChIPseq总共也就3个月的时间,做的事情并不多,在一知半解的情况下写下了ChIPseeker包。

正如我在《话题投票》里说的,我当时被要求做ChIPseq分析是为他人做嫁衣,而且是完全白干那种,但做为学生,白干也得干。

当时一开始使用ChIPpeakAnno做注释,但用UCSC genome browser检验结果的时候,发现对不上。在对ChIPpeakAnno包不满意的情况下,开始着手写ChIPseeker,其实在使用ChIPpeakAnno的时候,我就有写代码对结果做一些可视化,所以未有ChIPseeker先有ChIPseeker的部分可视化功能。当时写了篇博客文说ChIPpeakAnno的问题,一个月后就在Bioconductor上发表了ChIPseeker,这包完全是我半夜在宿舍里写出来的。

当时还在生物系,被我炒掉的前老板每天要求必须起码在实验[……]

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ChIPseeker for ChIP peak annotation (转贴)

https://guangchuangyu.github.io/2014/04/chipseeker-for-chip-peak-annotation/

ChIPpeakAnno WAS the only R package for ChIP peak annotation. I used it for annotating peak in my recent study.

I found it does not consider the strand information of genes. I reported the bug to the authors, but they are reluctant to change.

So I decided to develop my own package, ChIPseeker, and it’s now available in Bioconductor.

> require(TxDb.Hsapiens.UCSC.hg19.knownGene)
> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
> require(ChIPseeker)
> peakfile = getSampleFiles()[[4]]
> peakfile[......]

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