生物信息学常见1000个软件的安装代码！

昨天发推文后，很多朋友问这生物信息学常见1000个软件的安装代码啥意思。其实我在论坛发过，但是公众号很多人居然不知道我们的生信技能树论坛，只好搬过来一下！

安装软件是入行生物信息学着最常见的坑，毕竟你不得不用别人写的工具，但是写工具的人的水平参差不齐，所以必然有些难以安装，有些简单。

但是一定安装软件超过一定次数，你再回过头来看，就会觉得是非常简单的。 我这里把我安装的软件的所有代码全部共享出来，理论上，你只要是linux或者mac，就用我的代码就可以复现一下。

  1. ## annovar and GATK

  2. ## Download and install sratoolkit

  3. ## http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software

  4. ## http://www.ncbi.nlm.nih.gov/books/NBK158900/

  5. cd ~/biosoft

  6. mkdir sratoolkit &&  cd sratoolkit

  7. wget http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.6.3/sratoolkit.2.6.3-centos_linux64.tar.gz

  8. ##

  9. ##  Length: 63453761 (61M) [application/x-gzip]

  10. ##  Saving to: "sratoolkit.2.6.3-centos_linux64.tar.gz"

  11. tar zxvf sratoolkit.2.6.3-centos_linux64.tar.gz

  12. ~/biosoft/sratoolkit/sratoolkit.2.6.3-centos_linux64/bin/fastdump -h

  13. mkdir -p  ~/biosoft/myBin

  14. echo 'export PATH=/home/jianmingzeng/biosoft/myBin/bin:$PATH' >>~/.bashrc

  15. source ~/.bashrc

  16. cd ~/biosoft

  17. mkdir cmake &&  cd cmake

  18. wget http://cmake.org/files/v3.3/cmake-3.3.2.tar.gz

  19. tar xvfz cmake-3.3.2.tar.gz

  20. cd cmake-3.3.2

  21. ./configure --prefix=/home/jianmingzeng/biosoft/myBin

  22. make

  23. make install

  24. ## Download and install samtools

  25. ## http://samtools.sourceforge.net/

  26. ## http://www.htslib.org/doc/samtools.html

  27. cd ~/biosoft

  28. mkdir samtools &&  cd samtools

  29. wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2

  30. tar xvfj samtools-1.3.1.tar.bz2

  31. cd samtools-1.3.1

  32. ./configure --prefix=/home/jianmingzeng/biosoft/myBin

  33. make

  34. make install

  35. ~/biosoft/myBin/bin/samtools --help

  36. ~/biosoft/myBin/bin/plot-bamstats --help

  37. cd htslib-1.3.1

  38. ./configure --prefix=/home/jianmingzeng/biosoft/myBin

  39. make

  40. make install

  41. ~/biosoft/myBin/bin/tabix

  42. # ## Download and install tabix

  43. # cd ~/biosoft

  44. # mkdir tabix &&  cd tabix

  45. # # http://genometoolbox.blogspot.com/2013/11/installing-tabix-on-unix.html

  46. # tar xvfj tabix-0.2.6.tar.bz2

  47. # cd tabix-0.2.6

  48. # make

  49. # cd ~/biosoft

  50. # ## http://samtools.github.io/bcftools/

  51. # mkdir htslib &&  cd htslib  

  52. # git clone git://github.com/samtools/htslib.git

  53. # cd htslib

  54. # make

  55. ## Download and install bcftools

  56. ## http://www.htslib.org/download/

  57. ## http://www.htslib.org/doc/bcftools-1.0.html

  58. cd ~/biosoft

  59. mkdir bcftools &&  cd bcftools

  60. wget https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2

  61. tar xvfj bcftools-1.3.1.tar.bz2

  62. cd bcftools-1.3.1

  63. make

  64. cp bcftools /home/jianmingzeng/biosoft/myBin

  65. ~/biosoft/myBin/bin/bcftools --help

  66. ## Download and install vcftools

  67. ## https://vcftools.github.io/index.html

  68. ## http://vcftools.sourceforge.net/specs.html

  69. cd ~/biosoft

  70. mkdir vcftools &&  cd vcftools

  71. # wget https://codeload.github.com/vcftools/vcftools/legacy.zip/master -O  vcftools-vcftools-v0.1.14-24-gac1bfd5.zip

  72. # unzip vcftools-vcftools-v0.1.14-24-gac1bfd5.zip

  73. # mv vcftools-vcftools-ac1bfd5 vcftools-v0.1.14-24

  74. # cd vcftools-v0.1.14-24

  75. # export PERL5LIB=/home/jianmingzeng/biosoft/vcftools/vcftools-v0.1.14-24/src/perl/

  76. # ./autogen.sh

  77. # ./configure     --prefix=/home/jianmingzeng/biosoft/myBin

  78. # make

  79. # make install

  80. # ~/biosoft/myBin/bin/vcftools --help

  81. wget https://sourceforge.net/projects/vcftools/files/vcftools_0.1.13.tar.gz

  82. tar zxvf vcftools_0.1.13.tar.gz

  83. cd  vcftools_0.1.13

  84. make

  85. ## Download and install ANNOVAR  

  86. cd ~/biosoft

  87. # The latest version of ANNOVAR (2016Feb01) can be downloaded here (registration required)

  88. # http://www.openbioinformatics.org/annovar/annovar_download_form.php

  89. mkdir ANNOVAR  &&  cd ANNOVAR  

  90. ## Download and install samstat

  91. ## http://samstat.sourceforge.net/

  92. ## http://www.htslib.org/doc/samtools.html

  93. cd ~/biosoft

  94. mkdir samstat &&  cd samstat

  95. wget http://liquidtelecom.dl.sourceforge.net/project/samstat/samstat-1.5.tar.gz

  96. tar zxvf  samstat-1.5.tar.gz

  97. cd samstat-1.5

  98. ./configure --prefix=/home/jianmingzeng/biosoft/myBin

  99. make

  100. make install

  101. ~/biosoft/myBin/bin/samstat --help

  102. ## Download and install picardtools

  103. ## https://sourceforge.net/projects/picard/

  104. ## https://github.com/broadinstitute/picard

  105. cd ~/biosoft

  106. mkdir picardtools &&  cd picardtools

  107. wget http://ncu.dl.sourceforge.net/project/picard/picard-tools/1.119/picard-tools-1.119.zip

  108. unzip picard-tools-1.119.zip

  109. ## Download and install freebayes

  110. ## https://github.com/ekg/freebayes

  111. ## http://clavius.bc.edu/~erik/CSHL-advanced-sequencing/freebayes-tutorial.html

  112. cd ~/biosoft

  113. mkdir freebayes &&  cd freebayes

  114. ## wget -O freebayes-master.zip  https://codeload.github.com/ekg/freebayes/zip/master

  115. ## unzip freebayes-master.zip

  116. wget http://clavius.bc.edu/~erik/freebayes/freebayes-5d5b8ac0.tar.gz

  117. tar xzvf freebayes-5d5b8ac0.tar.gz

  118. cd freebayes

  119. make

  120. ~/biosoft/freebayes/freebayes/bin/freebayes

  121. cd ~/biosoft

  122. ## https://sourceforge.net/projects/varscan/files/

  123. ## http://varscan.sourceforge.net/index.html

  124. mkdir VarScan  &&  cd VarScan  

  125. wget https://sourceforge.net/projects/varscan/files/VarScan.v2.3.9.jar

  126. cd ~/biosoft

  127. mkdir SnpEff &&  cd SnpEff

  128. ##  http://snpeff.sourceforge.net/

  129. ##  http://snpeff.sourceforge.net/SnpSift.html

  130. ##  http://snpeff.sourceforge.net/SnpEff_manual.html

  131. wget http://sourceforge.net/projects/snpeff/files/snpEff_latest_core.zip

  132. ## java -jar snpEff.jar download GRCh37.75

  133. ## java -Xmx4G -jar snpEff.jar -i vcf -o vcf GRCh37.75 example.vcf > example_snpeff.vcf

  134. unzip snpEff_latest_core.zip

  135. ## https://github.com/najoshi/sickle

  136. cd ~/biosoft

  137. mkdir sickle && cd sickle

  138. wget https://codeload.github.com/najoshi/sickle/zip/master -O sickle.zip

  139. unzip sickle.zip

  140. cd sickle-master

  141. make

  142. ~/biosoft/sickle/sickle-master/sickle -h

  143. cd ~/biosoft

  144. ## http://www.usadellab.org/cms/?page=trimmomatic

  145. ## http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf

  146. mkdir Trimmomatic && cd Trimmomatic

  147. wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip

  148. unzip Trimmomatic-0.36.zip

  149. java -jar ~/biosoft/Trimmomatic/Trimmomatic-0.36/trimmomatic-0.36.jar -h

  150. ## Download and install bedtools

  151. cd ~/biosoft

  152. mkdir bedtools &&  cd bedtools

  153. wget https://github.com/arq5x/bedtools2/releases/download/v2.25.0/bedtools-2.25.0.tar.gz

  154. ## Length: 19581105 (19M) [application/octet-stream]

  155. tar -zxvf bedtools-2.25.0.tar.gz

  156. cd bedtools2

  157. make

  158. #~/biosoft/bedtools/bedtools2/bin/

  159. ## Download and install PeakRanger

  160. cd ~/biosoft

  161. mkdir PeakRanger &&  cd PeakRanger

  162. wget https://sourceforge.net/projects/ranger/files/PeakRanger-1.18-Linux-x86_64.zip

  163. ## Length: 1517587 (1.4M) [application/octet-stream]

  164. unzip PeakRanger-1.18-Linux-x86_64.zip

  165. ~/biosoft/PeakRanger/bin/peakranger -h

  166. ## Download and install bowtie

  167. cd ~/biosoft

  168. mkdir bowtie &&  cd bowtie

  169. wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.9/bowtie2-2.2.9-linux-x86_64.zip

  170. #Length: 27073243 (26M) [application/octet-stream]

  171. #Saving to: "download"   ## I made a mistake here for downloading the bowtie2

  172. mv download  bowtie2-2.2.9-linux-x86_64.zip

  173. unzip bowtie2-2.2.9-linux-x86_64.zip

  174. ## Download and install BWA

  175. cd ~/biosoft

  176. mkdir bwa &&  cd bwa

  177. #http://sourceforge.net/projects/bio-bwa/files/

  178. wget https://sourceforge.net/projects/bio-bwa/files/bwa-0.7.15.tar.bz2

  179. tar xvfj bwa-0.7.15.tar.bz2 # x extracts, v is verbose (details of what it is doing), f skips prompting for each individual file, and j tells it to unzip .bz2 files

  180. cd bwa-0.7.15

  181. make

  182. #export PATH=$PATH:/path/to/bwa-0.7.15 # Add bwa to your PATH by editing ~/.bashrc file (or .bash_profile or .profile file)

  183. # /path/to/ is an placeholder. Replace with real path to BWA on your machine

  184. #source ~/.bashrc

  185. ## Download and install macs2  

  186. ## // https://pypi.python.org/pypi/MACS2/

  187. cd ~/biosoft

  188. mkdir macs2 &&  cd macs2

  189. ## just stick to PyPI release: https://pypi.python.org/pypi/MACS2

  190. wget https://pypi.python.org/packages/9f/99/a8ac96b357f6b0a6f559fe0f5a81bcae12b98579551620ce07c5183aee2c/MACS2-2.1.1.20160309.tar.gz -O MACS2-2.1.1.tar.gz

  191. tar zxvf  MACS2-2.1.1.tar.gz

  192. cd  MACS2-2.1.1.20160309/

  193. python setup.py install --user

  194. ## https://docs.python.org/2/install/

  195. ~/.local/bin/macs2 --help

  196. #wget https://codeload.github.com/taoliu/MACS/zip/master -O MACS-master.zip

  197. #unzip MACS-master.zip

  198. #cd MACS-master

  199. ## So you can't just pull github snapshot then run setup.py to install MACS2. Instead

  200. # ImageMagick

  201. cd ~/biosoft

  202. mkdir ImageMagick &&  cd ImageMagick

  203. ## http://www.imagemagick.org/

  204. cd ~/biosoft

  205. mkdir weblogo &&  cd weblogo

  206. ## http://weblogo.berkeley.edu/

  207. wget http://weblogo.berkeley.edu/release/weblogo.2.8.2.tar.gz

  208. tar zxvf weblogo.2.8.2.tar.gz

  209. cd weblogo

  210. export PATH=$PATH:/home/jianmingzeng/biosoft/weblogo/weblogo

  211. source ~/.bashrc

  212. cd ~/biosoft

  213. mkdir Ghostscript &&  cd Ghostscript

  214. # http://www.ghostscript.com/download/gsdnld.html

  215. # http://www.ghostscript.com/doc/9.20/Readme.htm

  216. wget https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs920/ghostscript-9.20-linux-x86_64.tgz

  217. tar zxvf ghostscript-9.20-linux-x86_64.tgz

  218. cp ghostscript-9.20-linux-x86_64/gs-920-linux_x86_64  ~/biosoft/myBin/bin/gs

  219. ## make sure the "gs" program is executable

  220. ## Download and install homer (Hypergeometric Optimization of Motif EnRichment)

  221. ## // http://homer.salk.edu/homer/

  222. ## // http://blog.qiubio.com:8080/archives/3024

  223. ## The commands gs, seqlogo, blat, and samtools should now work from the command line

  224. cd ~/biosoft

  225. mkdir homer &&  cd homer

  226. wget http://homer.salk.edu/homer/configureHomer.pl

  227. perl configureHomer.pl -install

  228. perl configureHomer.pl -install hg19

  229. ## Download and install SWEMBL

  230. cd ~/biosoft

  231. mkdir SWEMBL &&  cd SWEMBL

  232. #### readme: http://www.ebi.ac.uk/~swilder/SWEMBL/beginners.html

  233. wget http://www.ebi.ac.uk/~swilder/SWEMBL/SWEMBL.3.3.1.tar.bz2

  234. tar xvfj SWEMBL.3.3.1.tar.bz2

  235. cd SWEMBL.3.3.1/

  236. make

  237. ## error

  238. ## Download and install SISSRs

  239. cd ~/biosoft

  240. mkdir SISSRs &&  cd SISSRs

  241. #### readme: https://dir.nhlbi.nih.gov/papers/lmi/epigenomes/sissrs/SISSRs-Manual.pdf

  242. wget http://dir.nhlbi.nih.gov/papers/lmi/epigenomes/sissrs/sissrs_v1.4.tar.gz

  243. tar xzvf sissrs_v1.4.tar.gz

  244. ~/biosoft/SISSRs/sissrs.pl

  245. ## Download and install SISSRs

  246. cd ~/biosoft

  247. mkdir QuEST &&  cd QuEST

  248. #### http://mendel.stanford.edu/SidowLab/downloads/quest/

  249. wget http://mendel.stanford.edu/SidowLab/downloads/quest/QuEST_2.4.tar.gz

  250. tar xzvf QuEST_2.4.tar.gz

  251. cd QuEST_2.4

  252. ## Download and install fastqc

  253. cd ~/biosoft

  254. mkdir fastqc &&  cd fastqc

  255. wget http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/fastqc_v0.11.5.zip

  256. unzip fastqc_v0.11.5.zip

  257. ## Download and install CEAS    

  258. ## http://liulab.dfci.harvard.edu/CEAS/download.html

  259. cd ~/biosoft

  260. mkdir CEAS  &&  cd CEAS

  261. wget  http://liulab.dfci.harvard.edu/CEAS/src/CEAS-Package-1.0.2.tar.gz

  262. tar zxvf CEAS-Package-1.0.2.tar.gz

  263. cd  CEAS-Package-1.0.2

  264. python setup.py install --user

  265. ## http://liulab.dfci.harvard.edu/CEAS/usermanual.html

  266. ~/.local/bin/ceas --help  

  267. mkdir annotation  &&  cd annotation  

  268. wget http://liulab.dfci.harvard.edu/CEAS/src/hg19.refGene.gz ; gunzip hg19.refGene.gz

  269. # http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz ##  gunzip refGene.txt.gz ; mv refGene.txt  hg19refGene.txt

  270. ## Download and install CEAS    

  271. ## http://liulab.dfci.harvard.edu/CEAS/download.html

  272. cd ~/biosoft

  273. mkdir crossmap  &&  cd crossmap

  274. pip install CrossMap --user

  275. ## http://crossmap.sourceforge.net/#use-pip-to-install-crossmap

  276. mkdir chain_files  &&  cd chain_files  

  277. wget http://hgdownload.soe.ucsc.edu/goldenPath/mm10/liftOver/mm10ToMm9.over.chain.gz

  278. wget http://hgdownload.soe.ucsc.edu/goldenPath/mm9/liftOver/mm9ToMm10.over.chain.gz

  279. wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz

  280. wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz

  281. # http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz ##  gunzip refGene.txt.gz ; mv refGene.txt  hg19refGene.txt

  282. # Usage: CrossMap.py bed ~/biosoft/crossmap/chain_files/mm9ToMm10.over.chain.gz  test.mm9.bed3

  283. cd ~/biosoft

  284. # http://www.broadinstitute.org/cancer/cga/rnaseqc_run

  285. # http://www.broadinstitute.org/cancer/cga/rnaseqc_download

  286. mkdir RNA-SeQC  &&  cd RNA-SeQC

  287. #### readme: http://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/rnaseqc/RNA-SeQC_Help_v1.1.2.pdf

  288. wget http://www.broadinstitute.org/cancer/cga/tools/rnaseqc/RNA-SeQC_v1.1.8.jar

  289. #TopHat+Cufflinks+ pipeline

  290. ## Download and install TopHat

  291. # https://ccb.jhu.edu/software/tophat/index.shtml

  292. cd ~/biosoft

  293. mkdir TopHat  &&  cd TopHat

  294. #### readme: https://ccb.jhu.edu/software/tophat/manual.shtml

  295. wget https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.Linux_x86_64.tar.gz

  296. tar xzvf tophat-2.1.1.Linux_x86_64.tar.gz

  297. ln -s tophat-2.1.1.Linux_x86_64 current

  298. # ~/biosoft/TopHat/current/tophat2

  299. ## Download and install Cufflinks

  300. #  http://cole-trapnell-lab.github.io/cufflinks/

  301. cd ~/biosoft

  302. mkdir Cufflinks  &&  cd Cufflinks

  303. #### readme: http://cole-trapnell-lab.github.io/cufflinks/manual/

  304. #### install:http://cole-trapnell-lab.github.io/cufflinks/install/

  305. wget http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz

  306. tar xzvf cufflinks-2.2.1.Linux_x86_64.tar.gz

  307. ln -s cufflinks-2.2.1.Linux_x86_64 current

  308. ~/biosoft/Cufflinks/current/cufflinks

  309. #HISAT-Stringtie2-Ballgown pipeline

  310. ## Download and install HISAT

  311. # https://ccb.jhu.edu/software/hisat2/index.shtml

  312. cd ~/biosoft

  313. mkdir HISAT  &&  cd HISAT

  314. #### readme: https://ccb.jhu.edu/software/hisat2/manual.shtml

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

  316. unzip hisat2-2.0.4-Linux_x86_64.zip

  317. ln -s hisat2-2.0.4  current

  318. ## ~/biosoft/HISAT/current/hisat2-build

  319. ## ~/biosoft/HISAT/current/hisat2  

  320. ## Download and install StringTie

  321. ## https://ccb.jhu.edu/software/stringtie/  ## https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual

  322. cd ~/biosoft

  323. mkdir StringTie &&  cd StringTie

  324. wget http://ccb.jhu.edu/software/stringtie/dl/stringtie-1.2.3.Linux_x86_64.tar.gz

  325. tar zxvf  stringtie-1.2.3.Linux_x86_64.tar.gz

  326. ln -s stringtie-1.2.3.Linux_x86_64 current

  327. # ~/biosoft/StringTie/current/stringtie

  328. cd ~/biosoft

  329. mkdir RSEM &&  cd RSEM

  330. wget https://codeload.github.com/deweylab/RSEM/tar.gz/v1.2.31

  331. mv v1.2.31  RSEM.v1.2.31.tar.gz

  332. tar zxvf RSEM.v1.2.31.tar.gz  

  333. ## Download and install HTSeq  

  334. ## http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html

  335. ## https://pypi.python.org/pypi/HTSeq

  336. cd ~/biosoft

  337. mkdir HTSeq &&  cd HTSeq

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

  339. tar zxvf HTSeq-0.6.1.tar.gz

  340. cd HTSeq-0.6.1

  341. python setup.py install --user

  342. ~/.local/bin/htseq-count  --help

  343. ## ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M1/

  344. ## http://hgdownload-test.cse.ucsc.edu/goldenPath/mm10/liftOver/

  345. ## GRCm38/mm10 (Dec, 2011)

  346. ## ls *bam |while read id;do ( ~/.local/bin/htseq-count  -f bam  $id   genecode/mm9/gencode.vM1.annotation.gtf.gz  1>${id%%.*}.gene.counts ) ;done

  347. ## ls *bam |while read id;do ( ~/.local/bin/htseq-count  -f bam -i exon_id  $id   genecode/mm9/gencode.vM1.annotation.gtf.gz  1>${id%%.*}.exon.counts ) ;done

  348. ## Download and install kallisto

  349. ## https://pachterlab.github.io/kallisto/starting

  350. cd ~/biosoft

  351. mkdir kallisto &&  cd kallisto

  352. wget https://github.com/pachterlab/kallisto/releases/download/v0.43.0/kallisto_linux-v0.43.0.tar.gz

  353. #tar zxvf  

  354. ## Download and install Sailfish

  355. ## http://www.cs.cmu.edu/~ckingsf/software/sailfish/  ##

  356. cd ~/biosoft

  357. mkdir Sailfish &&  cd Sailfish

  358. wget   https://github.com/kingsfordgroup/sailfish/releases/download/v0.9.2/SailfishBeta-0.9.2_DebianSqueeze.tar.gz

  359. #tar zxvf  

  360. ## Download and install salmon

  361. ## http://salmon.readthedocs.io/en/latest/salmon.html ##

  362. cd ~/biosoft

  363. mkdir salmon &&  cd salmon

  364. ## https://github.com/COMBINE-lab/salmon

  365. #tar zxvf  

  366. cd ~/biosoft

  367. mkdir GDC  &&  cd GDC  

  368. # https://gdc.cancer.gov/access-data/gdc-data-transfer-tool

  369. # http://gdc-docs.nci.nih.gov/Data_Transfer_Tool/Users_Guide/Getting_Started/

  370. wget https://gdc.nci.nih.gov/files/public/file/gdc-client_v1.2.0_Ubuntu14.04_x64.zip

  371. unzip gdc-client_v1.2.0_Ubuntu14.04_x64.zip

  372. cd ~/biosoft/myBin/bin

  373. ## http://hgdownload.cse.ucsc.edu/admin/exe/

  374. wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed

  375. wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedSort

  376. wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig

  377. wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes

  378. wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/wigToBigWig

  379. wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver

  380. wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigToBedGraph

  381. wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigBedToBed

  382. wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat

  383. wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/gfClient

  384. wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/gfServer

  385. ## Download and install variationtoolkit

  386. ## https://code.google.com/archive/p/variationtoolkit/downloads

  387. cd ~/biosoft

  388. mkdir variationtoolkit &&  cd variationtoolkit  

  389. wget https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/variationtoolkit/archive.tar.gz

  390. tar zxvf archive.tar.gz

  391. cd variationtoolkit

  392. make

  393. ## Download and install transvar

  394. # http://bioinformatics.mdanderson.org/main/Transvar

  395. cd ~/biosoft

  396. # https://bitbucket.org/wanding/transvar

  397. mkdir transvar &&  cd transvar  

  398. wget https://bitbucket.org/wanding/transvar/get/v2.1.19.20160221.zip

  399. unzip v2.1.19.20160221.zip

  400. cd wanding-transvar-5dd8a7366999

  401. python setup.py install --user

  402. cd ~/biosoft

  403. # http://kobas.cbi.pku.edu.cn/download.php

  404. mkdir kobas &&  cd kobas  

  405. # wget http://kobas.cbi.pku.edu.cn/download_file.php?type=seq_pep&filename=hsa.pep.fasta.gz

  406. # wget http://kobas.cbi.pku.edu.cn/download_file.php?type=sqlite3&filename=hsa.db.gz

  407. wget http://kobas.cbi.pku.edu.cn/kobas-2.1.1/kobas-2.1.1.tar.gz

  408. tar zxvf kobas-2.1.1.tar.gz

  409. cd kobas-2.1.1_20160822

  410. # * Download the KOBAS organism data package (organism.db.gz) from KOBAS Backend databases download website

  411. # * Download the KOBAS specific species data package from KOBAS Backend databases download website (for example, hsa.db.gz)

  412. # * Download the specific sequence file from KOBAS sequence files download website (for example, hsa.pep.fasta.gz)

  413. # * `gunzip organism.db.gz`

  414. # * `gunzip hsa.db.gz`

  415. # * Move all databases into ${kobas_home}/sqlite3/ (for example, organism.db, hsa.db)

  416. # * `gunzip hsa.pep.fasta.gz`

  417. # * Move the fasta sequence file into ${kobas_home}/seq_pep/

  418. # * `makeblastdb -in hsa.pep.fasta -dbtype prot`

  419. pip install RPy2 --user

  420. pip install Numpy --user

  421. pip install Pandas --user

  422. pip install BioPython --user

  423. pip install matplotlib --user

  424. pip install PySQLite --user

  425. source("http://bioconductor.org/biocLite.R")

  426. biocLite("qvalue")

  427. ## Download and install bamtools

  428. ## https://github.com/pezmaster31/bamtools/wiki/Building-and-installing

  429. cd ~/biosoft

  430. mkdir bamtools &&  cd bamtools  

  431. git clone git://github.com/pezmaster31/bamtools.git

  432. cd bamtools

  433. cmake --version  ## BamTools requires CMake (version >= 2.6.4).

  434. mkdir build &&  cd build

  435. cmake ../

  436. make

  437. ~/biosoft/bamtools/bamtools/bin/bamtools

  438. ## Download and install BAMStats

  439. ## http://bamstats.sourceforge.net/

  440. ## https://sourceforge.net/projects/bamstats/files/

  441. cd ~/biosoft

  442. mkdir BAMStats &&  cd BAMStats  

  443. wget https://nchc.dl.sourceforge.net/project/bamstats/BAMStats-1.25.zip

  444. unzip BAMStats-1.25.zip

  445. #java -jar  ~/biosoft/BAMStats/BAMStats-1.25/BAMStats-1.25.jar  --help

  446. ## Download and install Qualimap

  447. ## http://qualimap.bioinfo.cipf.es/

  448. cd ~/biosoft

  449. mkdir Qualimap &&  cd Qualimap  

  450. wget https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.2.1.zip

  451. ## readme  http://qualimap.bioinfo.cipf.es/doc_html/index.html

  452. ## example results :http://kokonech.github.io/qualimap/HG00096.chr20_bamqc/qualimapReport.html

  453. unzip qualimap_v2.2.1.zip

  454. ~/biosoft/bamtools/bamtools/bin/bamtools

  455. ~/biosoft/Qualimap/qualimap_v2.2.1/qualimap --help ## --java-mem-size=4G

  456. ## modify ~/.bashrc by adding PATH=$PATH:~/.local/bin/

  457. ## Download and install deepTools

  458. ## https://github.com/fidelram/deepTools

  459. ## http://deeptools.readthedocs.io/en/latest/content/example_usage.html

  460. pip install pyBigWig --user

  461. cd ~/biosoft

  462. mkdir deepTools &&  cd deepTools  

  463. git clone https://github.com/fidelram/deepTools ## 130M,

  464. cd deepTools

  465. python setup.py install --user

  466. ## 17 tools in ~/.local/bin/

  467. ~/.local/bin/deeptools

  468. cd ~/biosoft

  469. mkdir ngsplot &&  cd ngsplot  

  470. ## download by yourself :https://drive.google.com/drive/folders/0B1PVLadG_dCKN1liNFY0MVM1Ulk  

  471. tar -zxvf ngsplot-2.61.tar.gz

  472. tar zxvf ngsplot.eg.bam.tar.gz

  473. echo 'export PATH=/home/jianmingzeng/biosoft/ngsplot/ngsplot/bin:$PATH' >>~/.bashrc  

  474. echo 'export NGSPLOT=/home/jianmingzeng/biosoft/ngsplot/ngsplot' >>~/.bashrc

  475. source ~/.bashrc

  476. install.packages("doMC", dep=T)

  477. install.packages("caTools", dep=T)

  478. install.packages("utils", dep=T)

  479. source("http://bioconductor.org/biocLite.R")

  480. biocLite( "BSgenome" )

  481. biocLite( "Rsamtools" )

  482. biocLite( "ShortRead" )

  483. cd ~/biosoft

  484. mkdir breakdancer &&  cd breakdancer  

  485. # http://breakdancer.sourceforge.net/

  486. # you need to install 2 perl module by yourself : http://breakdancer.sourceforge.net/moreperl.html

  487. wget https://sourceforge.net/projects/breakdancer/files/breakdancer-1.1.2_2013_03_08.zip

  488. unzip breakdancer-1.1.2_2013_03_08.zip

  489. cd breakdancer-1.1.2/cpp

  490. make  ##something wrong !

  491. ## usage: http://breakdancer.sourceforge.net/pipeline.html

  492. cd ~/biosoft

  493. # http://boevalab.com/FREEC/

  494. mkdir Control-FREEC && cd Control-FREEC

  495. # https://github.com/BoevaLab/FREEC/releases

  496. wget https://github.com/BoevaLab/FREEC/archive/v10.3.zip

  497. unzip v10.3.zip

  498. # https://www.ncbi.nlm.nih.gov/pubmed/22155870

  499. # http://boevalab.com/FREEC/tutorial.html

  500. # http://samtools.sourceforge.net/pileup.shtml

  501. cd ~/biosoft

  502. # https://github.com/dellytools/delly

  503. mkdir delly && cd delly

  504. # git clone --recursive https://github.com/dellytools/delly.git

  505. # cd delly

  506. # make all

  507. # make PARALLEL=1 -B src/delly

  508. wget https://github.com/dellytools/delly/releases/download/v0.7.6/delly_v0.7.6_linux_x86_64bit

  509. chmod 777 delly_v0.7.6_linux_x86_64bit

  510. ~/biosoft/delly/delly_v0.7.6_linux_x86_64bit  --help

  511. ## delly call -t DEL -g hg19.fa -o s1.bcf -x hg19.excl sample1.bam

  512. ## ./delly/src/bcftools/bcftools view delly.bcf > delly.vcf

  513. ## The SV type can be DEL, DUP, INV, TRA, or INS for deletions, tandem duplications, inversions, translocations and small insertions, respectively.

  514. ## In addition, you can filter input reads more stringently using -q 20 and -s 15.

  515. cd ~/biosoft

  516. # https://www.cog-genomics.org/plink2/data#merge_list

  517. mkdir PLINK && cd PLINK

  518. wget https://www.cog-genomics.org/static/bin/plink170113/plink_linux_x86_64.zip

  519. unzip plink_linux_x86_64.zip

  520. ~/biosoft/PLINK/plink

  521. ## Download and install Scalpel

  522. cd ~/biosoft

  523. mkdir Scalpel &&  cd Scalpel

  524. wget https://downloads.sourceforge.net/project/scalpel/scalpel-0.5.3.tar.gz  

  525. tar zxvf scalpel-0.5.3.tar.gz

  526. cd scalpel-0.5.3

  527. make

  528. ~/biosoft/Scalpel/scalpel-0.5.3/scalpel-discovery  --help

  529. ~/biosoft/Scalpel/scalpel-0.5.3/scalpel-export  --help

  530. cd ~/biosoft

  531. # https://www.cog-genomics.org/plink2/data#merge_list

  532. mkdir firehose && cd firehose

  533. wget http://gdac.broadinstitute.org/runs/code/firehose_get_latest.zip

  534. unzip firehose_get_latest.zip

  535. ~/biosoft/firehose/firehose_get

  536. ~/biosoft/firehose/firehose_get -tasks clinical analyses latest brca

  537. cd ~/biosoft

  538. # https://www.cog-genomics.org/plink2/data#merge_list

  539. mkdir fastpop && cd fastpop

  540. wget https://sourceforge.net/projects/fastpop/files/FastPop.tar.gz

  541. wget https://jaist.dl.sourceforge.net/project/fastpop/FastPop_Instruction.pdf

  542. tar zxvf FastPop.tar.gz  

  543. pip install cnvkit --user

再来一个转录组 de novo分析流程的软件全代码安装咯： Trinotate/Trinity/TransDecoder/sqlite/NCBI BLAST+/HMMER/PFAM signalP v4 /tmhmm v2 /RNAMMER 有些软件需要教育邮箱注册才行哦~~

  1. ## Trinotate/Trinity/TransDecoder/sqlite/NCBI BLAST+/HMMER/PFAM

  2. ## signalP v4 /tmhmm v2 /RNAMMER

  3. cd ~/biosoft

  4. mkdir hmmer &&  cd hmmer

  5. wget http://eddylab.org/software/hmmer/2.3/hmmer-2.3.tar.gz

  6. tar zxvf hmmer-2.3.tar.gz

  7. cd hmmer-2.3

  8. ./configure --prefix=/home/jmzeng/my-bin

  9. #./configure --prefix=/home/jianmingzeng/biosoft/myBin

  10. make

  11. make install

  12. #for file in hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch ; do\

  13. #      cp src/$file /home/jmzeng/my-bin/bin/;\

  14. #   done

  15. #for file in hmmer hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch; do\

  16. #      cp documentation/man/$file.man /home/jmzeng/my-bin/man/man1/$file.1;\

  17. #   done

  18. cp /home/jmzeng/my-bin/bin/hmmsearch /home/jmzeng/my-bin/bin/hmmsearch2

  19. cd ~/biosoft

  20. mkdir CBS &&  cd CBS

  21. #   signalP v4 (free academic download) http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp

  22. #   tmhmm v2 (free academic download) http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm

  23. #   RNAMMER (free academic download) http://www.cbs.dtu.dk/cgi-bin/sw_request?rnammer

  24. mkdir signalp-4.1

  25. mkdir rnammer-1.2

  26. ## be sure to untar it in a new directory

  27. ## it's a perl script, we need to modify it according to readme http://trinotate.github.io/#SoftwareRequired

  28. ## vi ~/biosoft/CBS/signalp-4.1/signalp

  29. tar zxvf signalp-4.1e.Linux.tar.gz

  30. tar zxvf rnammer-1.2.src.tar.Z

  31. tar zxvf tmhmm-2.0c.Linux.tar.gz

  32. ## it's a perl script, we need to modify it according to readme http://trinotate.github.io/#SoftwareRequired

  33. ## vi ~/biosoft/CBS/tmhmm-2.0c/bin/tmhmm

  34. ## vi ~/biosoft/CBS/tmhmm-2.0c/bin/tmhmmformat.pl

  35. which perl  ## /usr/bin/perl

  36. cd ~/biosoft

  37. mkdir blastPlus &&  cd blastPlus

  38. #   ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST

  39. wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.5.0+-x64-linux.tar.gz

  40. blastBinFolder=~/biosoft/blastPlus/ncbi-blast-2.5.0+/bin

  41. $blastBinFolder/makeblastdb -help

  42. #   http://www.cbs.dtu.dk/services/doc/signalp-4.1.readme

  43. cd ~/biosoft

  44. mkdir TransDecoder &&  cd TransDecoder

  45. #   https://transdecoder.github.io/

  46. # https://github.com/TransDecoder/TransDecoder/releases

  47. wget https://github.com/TransDecoder/TransDecoder/archive/v3.0.0.tar.gz  -O TransDecoder.v3.0.0.tar.gz

  48. tar zxvf TransDecoder.v3.0.0.tar.gz

  49. cd TransDecoder-3.0.0

  50. make

  51. ~/biosoft/TransDecoder/TransDecoder-3.0.0/TransDecoder.LongOrfs -h

  52. ~/biosoft/TransDecoder/TransDecoder-3.0.0/TransDecoder.Predict -h

  53. ## sqlite3  --help

  54. cd ~/biosoft

  55. mkdir Trinotate &&  cd Trinotate

  56. #   http://trinotate.github.io/

  57. #   https://github.com/Trinotate/Trinotate/releases

  58. wget https://github.com/Trinotate/Trinotate/archive/v3.0.1.tar.gz  -O Trinotate.v3.0.1.tar.gz

  59. tar zxvf Trinotate.v3.0.1.tar.gz

  60. ~/biosoft/Trinotate/Trinotate-3.0.1/Trinotate -h

  61. wget https://data.broadinstitute.org/Trinity/Trinotate_v3_RESOURCES/Pfam-A.hmm.gz

  62. wget https://data.broadinstitute.org/Trinity/Trinotate_v3_RESOURCES/uniprot_sprot.pep.gz

  63. wget https://data.broadinstitute.org/Trinity/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz  -O Trinotate.sqlite.gz

  64. gunzip Trinotate.sqlite.gz

  65. gunzip uniprot_sprot.pep.gz

  66. makeblastdb -in uniprot_sprot.pep -dbtype prot

  67. gunzip Pfam-A.hmm.gz

  68. hmmpress Pfam-A.hmm

当然啦，代码没有一千个，但是是在持续累积的，只要我用过的软件我都记录下来了。 ！

软件安装在我看来分成3类

  • 第一就是二进制可执行程序，直接下载软件包解压后就可以全路径调用啦！

  • 第二就是所有的语言代码啦，比如perl,R,python,java,matlab,ruby,C等等 其中C源码就是./configure,make,make install，也有的就是make，取决于readme，这个也是报错最多的，一般就是没有权限，缺库，很头疼。 然后perl和python软件呢，主要就是模块依赖的问题。 R，java,软件非常简单了。 matlab软件，你要是在windows界面用到还好，想去linux用，也折腾好几个星期。 ruby其它我没有用过啦。

  • 最后就是系统或者语言自带的各种软件中心安装器啦，apt-get，yum，bioconda，cpan，cran，pip等等

其实前些天的推文，我讲到了很多软件安装的基础知识，如果你只需要收藏代码，就不需要看啦。计算资源及编程-仅针对生信人员

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