/
howtoInstall
executable file
·79 lines (53 loc) · 2.21 KB
/
howtoInstall
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
Installare:
Java ORACLE, --> must be set with "sudo update-alternatives --config java "
Rstudio,
R devel,
git,
openssl-devel
libcurl-devel
R
install.packages("git2r")
install.packages("httr")
install.packages("devtools")
source("https://bioconductor.org/biocLite.R"
biocLite("DESeq2")
biocLite("RnaSeqSampleSize")
library(devtools)
install_github("kendomaniac/docker4seq")
utente docker
fare partire il demone:
sudo systemctl start docker
installare i docker:
sudo docker pull docker.io/rcaloger/annotate.2017.01
sudo docker pull docker.io/rcaloger/bwa.2017.01
sudo docker pull docker.io/rcaloger/chipseq.2017.01
sudo docker pull docker.io/rcaloger/mirnaseq.2017.01
sudo docker pull docker.io/rcaloger/rsemstar.2017.01
sudo docker pull docker.io/rcaloger/skewer.2017.01
installare vnc-server
creare file: /etc/systemd/system/vncserver@:2.service
contenuto file:
[Unit]
Description=Remote desktop service (VNC)
After=syslog.target network.target
[Service]
Type=simple
User=user
PIDFile=/home/user/.vnc/%H%i.pid
ExecStartPre=/bin/sh -c '/usr/bin/vncserver -kill %i > /dev/null 2>&1 || :'
ExecStart=/usr/bin/vncserver :2 -geometry 1024x768 -alwaysshared -fg
ExecStop=/usr/bin/vncserver -kill :2
[Install]
WantedBy=multi-user.target
Settare password vnc user
Settare boot esecutio:
sudo systemctl enable vncserver@:2.service
testing:
nohup R CMD BATCH script.R &
library(docker4seq)
rsemstarIndex(group="sudo",genome.folder="/data/scratch/hg38star", ensembl.urlgenome="ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz", ensembl.urlgtf="ftp://ftp.ensembl.org/pub/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh38.87.gtf.gz", threads=8)
library(docker4seq)
system("wget http://130.192.119.59/public/test_R1.fastq.gz")
system("wget http://130.192.119.59/public/test_R2.fastq.gz")
rnaseqCounts(group="sudo",fastq.folder=getwd(), scratch.folder="/data/scratch", adapter5="AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT", adapter3="AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT", seq.type="pe", threads=8, min.length=40, genome.folder="/data/scratch/hg38star", strandness="none", truncating.expected.counts=FALSE, annotation.type="gtfENSEMBL")
R command