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Biostack R系列服务器

当前戴尔销售的服务器为第13代,高性能计算中使用比较多的为R730,14代服务器应该也会于Q4发布,但是一些公司,比如游戏公司,会不断对服务器升级,并下架那些老一代的服务器,那些下架机器仍然具有很好的性能。

现阶段学习生物信息越来越受到关注,而学习生物信息最快的途径就是实战,亲自去编写程序或去使用生物信息应用解决生物信息学问题,这样就需要有学习的软件和硬件环境。

最新更新

2017-07-12 嵌入 div_seq_lite 数据分析流程
  10个样本(每个样本平均3W条序列)的数据可以在1.5分钟完成解析。 核心功能全部使用 Usearch, 主要功能包括:
      1. 序列修剪.
      2.双端序列合并
      3. 构建OTU表
      4. 去除叶绿体线粒体 16S序列
      5. 菌群结构分布
      6. alpha多样性分析以及稀释曲线 
      7. beta多样性分析

标配价格

5800 人民币/台
注:1. 包运费
    2. 含税
    3. 主机(除额外配置SATA硬盘、以及8G/16G 内存以外)皆为DELL原装.
    4. 2T SATA硬盘、8G / 16G 内存为全新配件。
    5. 采用系统2块300G Raid1 镜像冗余,保证系统稳定性。
    6. Biostack软件独立一块2T盘,方便后期维护。
    7. 项目project目录独立,方便组Raid扩容。 

硬件配置

服务器安装配置:

处理器:2 * E5645 (2.40GHz),共计12核心、24线程
内存: 4  * 4G, 共计16G内存
阵列卡:1 * 6I阵列卡,支持Raid 0/1/5/10等
硬盘:2 * 300G 15K SAS盘
硬盘:2 * 2TB SATA盘
电源: 单电

软件配置

系统分区及其目录结构:

1. biostack分区, 安装应用和数据库
2. project分区, 数据和项目目录

账户系统###:

1. root 密码: biostack
2. 管理员用户: biostack, 密码:biostack

基础开发环境及其服务

采用CentOS 7 的开发者模式安装操作系统, C/C++编译器已经预安装

安装FTP服务器

目录结构:

1. FTP主目录, /project/pub
2. 用户主目录, /project/pub/用户名
3. 用户数据目录, /project/pub/用户名/pub

添加虚拟用户:

1. 修改: /etc/vsftpd/virtusers 文件, 添加用户和密码
2. 添加虚拟用户配置文件: 再 /etc/vsftpd/vconf 目录创建相对应的用户配置文件

更新生效:

db_load -T -t hash -f /etc/vsftpd/virtusers /etc/vsftpd/virtusers.db
systemctl restart  vsftpd.service

安装Samba服务器

根据需求添加Samba共享服务目录

修改/etc/samba/smb.conf 文件, 添加如下信息:

[project]
path = /biostack              #添加目录路径
public = yes
browsable = yes
valid users = @biostack      #限制用户组
writable = yes
guest ok = yes
read only = no
available = yes

更新生效:

sudo systemctl restart smb.service
sudo systemctl restart nmb.service

Perl 环境

预安装Perl模块列表:

App::cpanminus
Array::Utils
B::Hooks::EndOfScope
Capture::Tiny
Class::Data::Inheritable
Class::HPLOO
Class::Load
Class::Load::XS
Convert::Binary::C
CPAN::Meta
CPAN::Meta::Check
CPAN::Meta::YAML
Crypt::RC4
Cwd
Data
Data::OptList
DBD::SQLite
Devel::GlobalDestruction
Devel::OverloadInfo
Devel::StackTrace
Digest::Perl::MD5
Dist::CheckConflicts
Encode
Eval::Closure
Exception::Class
Exporter::Tiny
ExtUtils::PkgConfig
File::Find::Rule
File::Grep
File::Path
File::pushd
File::Slurper
File::Temp
File::Which
Getopt::Long
Graph
Graph::ReadWrite
HDB
HTML-TableExtract
IO::String
IO::Stringy
JSON::PP
List::MoreUtils
List::Util
Log::Log4perl
Module::Implementation
Module::Metadata
Module::Runtime::Conflicts
Moose
MRO::Compat
namespace::clean
Number::Compare
OLE::Storage_Lite
Package::DeprecationManager
Package::Stash
Package::Stash::XS
Params::Util
Parse::Yapp
PerlIO::utf8_strict
Spreadsheet::ParseExcel
Sub::Exporter
Sub::Exporter::Progressive
Sub::Identify
Sub::Install
Sub::Name
Sub::Uplevel
SVG
Switch
Test::CleanNamespaces
Test::Deep
Test::Exception
Test::Fatal
Test::Harness
Test::Most
Test::Needs
Test::Pod
Test::Requires
Test::Simple
Test::Warn
Test::Warnings
Text::CSV
Text::Glob
Try::Tiny
Variable::Magic
XML::DOM
XML::DOM::XPath
XML::Filter::BufferText
XML::RegExp
XML::SAX::Expat
XML::SAX::Writer
XML::Simple
XML::Writer
XML::XPathEngine
YAML::LibYAML

Python 环境

预安装Python模块列表:

attrdict
backports.shutil-get-terminal-size
backports.ssl-match-hostname
Beaker
biom-format
biome
biopython
blivet
brewer2mpl
Brlapi
burrito
burrito-fillings
cffi
chardet
click
cogent
configobj
configshell-fb
coverage
cryptography
cupshelpers
custodia
cycler
Cython
decorator
di
dnspython
docopt
emperor
enum34
ete3
ethtool
firstboot
freeipa
fros
funcsigs
future
ga4ghmongo
gdata
ggplot
gssapi
idna
iniparse
initial-setup
iotop
ipaclient
ipaddr
ipaddress
ipalib
ipaplatform
ipapython
IPy
ipython
ipython-genutils
javapackages
jwcrypto
kdcproxy
kitchen
kmod
langtable
lvm
lxml
M2Crypto
Magic-file-extensions
Mako
MarkupSafe
matplotlib
mock
mongoengine
mykatlas
mykrobe
MySQL-python
natsort
ncbi-genome-download
netaddr
netifaces
nose
ntplib
numpy
openlmi
pandas
Paste
pathlib
pathlib2
patsy
pbr
pcp
perf
pexpect
pickleshare
pip
ply
policycoreutils-default-encoding
prompt-toolkit
psycopg2
ptyprocess
pyasn1
pycparser
pycups
pycurl
Pygments
pygobject
pygpgme
pyinotify
pykickstart
pyliblzma
pymongo
pynast
pyOpenSSL
pyparsing
pyparted
pyqi
pysam
pysmbc
python-augeas
python-dateutil
python-dmidecode
python-ldap
python-meh
python-memcached
python-nss
python-yubico
pytz
pyudev
pyusb
PyVCF
pywbem
pyxattr
PyYAML
qcli
qiime
qiime-default-reference
qrcode
requests
rtslib-fb
scandir
scdate
scikit-bio
scipy
seaborn
seobject
sepolicy
setproctitle
setroubleshoot
setuptools
simplegeneric
six
slip
slip.dbus
SSSDConfig
statsmodels
targetcli-fb
targetd
Tempita
traitlets
urlgrabber
urllib3
urwid
virtualenv
wcwidth
wheel
XlsxWriter
yum-langpacks
yum-metadata-parser

R 环境

预安装R模块列表:

annotate
BiocGenerics
class
digest
GenomicFeatures
graphics
labeling
methods
pkgconfig
rlang
spatial
tools
zlibbioc
AnnotationDbi
BiocInstaller
cluster
docopt
GenomicRanges
grDevices
lambda.r
mgcv
plogr
rlist
splines
topGO
AnnotationForge
BiocParallel
codetools
dplyr
getopt
grid
lattice
mime
plyr
rpart
stats
translations
ape
biomaRt
colorspace
edgeR
ggplot2
GSEABase
lazyeval
munsell
qvalue
Rsamtools
stats4
utils
assertthat
Biostrings
compiler
foreign
ggtree
gtable
limma
nlme
R6
RSQLite
stringi
vegan
base
bit
curl
futile.logger
git2r
gtools
locfit
nnet
RBGL
rstudioapi
stringr
whisker
BH
bit64
datasets
futile.options
glue
hash
magrittr
openssl
RColorBrewer
rtracklayer
SummarizedExperiment
withr
BiasedUrn
bitops
data.table
genefilter
GO.db
httr
MASS
optparse
Rcpp
S4Vectors
survival
XML
bindr
blob
DBI
geneLenDataBase
goseq
IRanges
Matrix
parallel
RCurl
scales
tcltk
xtable
bindrcpp
boot
devtools
GenomeInfoDb
GOstats
jsonlite
matrixStats
permute
reshape
snow
tibble
XVector
Biobase
Category
dichromat
GenomicAlignments
graph
KernSmooth
memoise
pheatmap
reshape2
SparseM
tidyr
yaml

Biostack 原安装应用列表

原装应用:

bbmap-36.84
blast-2.2.26
blat-36
bowtie-1.2R
bowtie2-2.3.0
bwa-0.7.15
cd-hit-4.6.1
clustal-omega-1.2.3
diamond-0.8.37
hmmer-2.3.2
hmmer-3.1b2
infernal-1.1.2
mafft-7.222
snap-1.0dev.96
mauve-2.4.0
minimap-0.2
MUMmer-3.23
muscle-3.8.1551
ncbi-blast+-2.6.0
verticalize-0.0.1
prank-121218
RAPSearch-2.24
vsearch-2.4.2
bmtagger-3.102
KronaTools-2.7
mash-1.1.1
pplacer-1.1a18
ribopicker-0.4.3
sortmerna-2.1b
metaphlan2-2.6.0
uproc-2.0.0-rc1
bioawk-1.0
FastQC-0.11.5
fastq-tools-0.8
fastx_toolkit-0.0.14
FLASH-1.2.11
fqtools-2.0
jellyfish-1.1.11
jellyfish-2.2.6
seqkit-0.3.5
seqtk-1.2
sickle-1.33
sratoolkit-2.8.1
Trimmomatic-0.36
wgsim-0.3.1
jdk-1.7.0_80
jdk-1.8.0_111
R-3.3.3
bamtools-2.4.1
bcftools-1.4
bedtools2-2.26.0
htslib-1.4
igvtools-2.3.91
picard-2.9.0
sambamba-0.6.5
samblaster-0.1.23
samtools-0.1.18
samtools-1.4
EMBOSS-6.6.0
gargs-0.3.7
genometools-1.5.9
tabtk-0.1
csvtk-0.8.0
tsv-utils-1.1.11
parallel-20161022
htop-2.0.2
aspera-connect-3.6.1.110647
axel-2.11
gffread-0.9.6
pigz-2.3.4
xz-5.2.2
cufflinks-2.2.1
hisat2-2.0.5
transrate-1.0.3
kallisto-0.43.0
Rockhopper-2.0.3
RSEM-1.3.0
Salmon-0.8.2
STAR-2.5.3a
stringtie-1.3.3b
subread-1.5.1
tophat-2.1.1
TransDecoder-3.0.1
trinityrnaseq-2.2.0
idba-1.1.3
idba-mt-1.0
CAP3-021015
megahit-1.0.6.1
miniasm-0.2
SOAPdenovo2-240
SPAdes-3.9.1
velvet-1.2.10
VelvetOptimiser-2.2.5
andi-0.10
FastTree-2.1.9
Parsnp-1.2
phylip-3.696
trimal-1.4.1
abricate-0.3
ANIcalculator-1.0
aragorn-1.2.38
barrnap-0.7
eggnog-mapper-0.12.7
glimmer-3.02b
GlimmerHMM-3.0.4
mcl-14-137
augustus-3.2.3
BRAKER1-1.10
gm_et-4.33
prodigal-2.6.3
busco-3.0
tbl2asn-25.3
mlst-2.6
prokka-1.12
delly-0.7.6
freebayes-1.1.0
lumpy-sv-0.2.13
vcfanno-0.2.4
snp-sites-2.3.2
wham-1.8.0
snpEff-4.3
seqtk_utils-0.1.1
tabtk_utils-0.1.4
CNOGpro-utils-0.1.1
ImageMagick_utils-0.1.1
blast_utils-0.1.1
blobtools-0.9.19.3
taxonomy_utils-0.1.1
breseq-0.30.0
snippy-3.1
vcftools-0.1.14
go-1.8.1
boost-1.61.0
ksontk_utils-0.0.1
RGI-3.1.1
ResistoMap-0.0.x

Biostack 预安装数据库

数据库列表:

16SMicrobial
brenda
dbcan
eggnog-mapper
greengene
hg38
nr
pfam
RDP
rfam
sintax
swiss_prot
taxonomy
ardb
CARD
eggnog
gene_ontology
hg19
mash
nt
pynast_greengene
Resfams
silva
STRING
tax4fun
<p align = "right">来自Biostack团队: 2017-08-01 版本</p>