conda 报错 Solving environment: failed

现在说说我的解决思路: 1.根据错误内容,安装失败的原因应该是这个网址 https://repo.anaconda.com/pkgs/main/noarch/repodata.json.bz2 请求失败。 2.所以我尝试用 wget https://repo.anaconda.com/pkgs/main/noarch/repodata.json.bz2 1 手动下载这个包,结果出现以下错误。 -2018-12-12 18:29:18– https://repo.anaconda.com/pkgs/main/noarch/repodata.json.bz2 Connect[……]

Read more

[…]

ssh, scp and rsync

[Admin.DESKTOP-7JT504C] ➤ rsync -P –rsh=ssh /drives/d/Kraken_12.tar.gz cityu_jhli_1@172.16.22.11:/BIGDATA1/cityu_jhli_1/mhyleung/database/findfungi Warning: Permanently added ‘172.16.22.11’ (RSA) to the list of known hosts. rsync -P -avz -e “ssh -p5566 -i /drives/C/Users/Admin/Desktop/cityu_jhli[……]

Read more

[…]

v2ray

https://github.com/Jrohy/multi-v2ray  

Docker运行

默认创建mkcp + 随机一种伪装头配置文件:

docker run -d --name v2ray --privileged --restart always --network host jrohy/v2ray 

自定义v2ray配置文件:

docker run -d --name v2ray --privileged -v /path/config.json:/etc/v2ray/config.json --restart always --network host[......]

Read more

[…]

Multivariate analyses in R (PERMANOVA )

https://rpubs.com/collnell/manova

Multivariate analyses in R

By C Nell

Types of questions

Do groups differ in composition? Does community structure vary among regions or over time? Do environmental variables explain community patterns? Which species are responsible for differences among g[……]

Read more

[…]

Good software

multiqc   ranger    ployly https://github.com/MultiQC https://github.com/ranger/ranger https://zhuanlan.zhihu.com/p/34369349 […]

R drawing png with high resolution

可重复的示例:

the_plot <- function() { x <- seq(0, 1, length.out = 100) y <- pbeta(x, 1, 10) plot( x, y, xlab = "False Positive Rate", ylab = "Average true positive rate", type = "l" ) }

 

png( "test.png", width = 3.25, height = 3.25,[......]

Read more

[…]

tmap install

  1199 git clone https://github.com/GPZ-Bioinfo/tmap.git 1200 cd tmap 1201 ll 1202 python setup.py install 1203 ll 1204 cd ../ 1205 rm -rf tmap 1206 deactivate 1207 rmvirtualenv tmap_ENV 1208 mkvirtualenv -p /usr/bin/python3.4m tmap_ENV pip3 install pypiwin32 conda install sci[……]

Read more

[…]

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/viru[……]

Read more

[…]

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[......]

Read more

[…]

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 im[......]

Read more

[…]