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kubu4 edited this page Jan 24, 2018 · 38 revisions

TOC

Computer: hummingbird

OS: OS X (10.9.5)

FastQC (0.11.2)

 path = /usr/local/bioinformatics/FastQC/

Trimmomatic (0.30)

 path = /usr/local/bioinformatics/Trimmomatic-0.30/

Trinotate (Release 2014-07-08)

 path = /usr/local/bioinformatics/Trinotate_r20140708/

bedtools (2.22.1)

 path = /usr/local/bioinformatics/bedtools-2.22.1/

bismark (0.14.2)

 path = /usr/local/bioinformatics/bismark_v0.14.2/

bowtie (1.0.0)

 path = /usr/local/bioinformatics/bowtie-1.0.0/

bowtie2 (2.1.0)

 path = /usr/local/bioinformatics/bowtie2-2.1.0/

cufflinks (2.2.1.OSX_x86_64)

 path = /usr/local/bioinformatics/cufflinks-2.2.1.OSX_x86_64/

fastx_toolkit (0.0.13.2)

 path = /usr/local/bioinformatics/fastx_toolkit-0.0.13.2/

hmmer (3.1b1)

 path = /usr/local/bioinformatics/hmmer-3.1b1/

libgtextutils (0.6.1)

 path = /usr/local/bioinformatics/libgtextutils-0.6.1/

ncbi-blast (2.2.29+)

 path = /usr/local/bioinformatics/ncbi-blast-2.2.29+/

ngsplot (2.08)

 path = /usr/local/bioinformatics/ngsplot-2.08/

rsem (1.2.10)

 path = /usr/local/bioinformatics/rsem-1.2.10/

signalp (4.1)

 path = /usr/local/bioinformatics/signalp-4.1/

stacks (1.13)

 path = /usr/local/bioinformatics/stacks-1.13/

tophat (2.0.13.OSX_x86_64)

 path = /usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/

trinity (Release 2013-11-10)

 path = /usr/local/bioinformatics/trinityrnaseq_r20131110/

ipython (3.0.0)

Geneious (5.3.6)

Computer: ostrich

OS: OS X (10.11.6)

FastQC (0.11.5)

 path = /Users/Shared/bioinformatics/FastQC/

Trimmomatic (0.30)

 path = /Users/Shared/bioinformatics/Trimmomatic-0.36/

Trinotate (3.0.1)

 path = /Users/Shared/bioinformatics/Trinotate-3.0.1/

bedtools (2.26.0)

 path = /Users/Shared/bioinformatics/bedtools2/

bismark (0.16.3)

 path = /Users/Shared/bioinformatics/bismark_v0.15.0/

bowtie (1.1.2)

 path = /Users/Shared/bioinformatics/bowtie1-1.1.2

bowtie2 (2.2.9)

 path = /Users/Shared/bioinformatics/bowtie2-2.2.9

celera assembler (8.3rc2)

path = /Users/Shared/bioinformatics/wgs-8.3rc2

cufflinks (2.2.1.OSX_x86_64)

 path = /Users/Shared/bioinformatics/cufflinks-2.2.1.OSX_x86_64

hmmer (3.1b2)

 path = /Users/Shared/bioinformatics/hmmer-3.1b2-macosx-intel

ncbi-blast (2.5.0)

 path = /Users/Shared/bioinformatics/ncbi-blast-2.5.0+

ngsplot (2.08)

 path = /Users/Shared/bioinformatics/ngsplot

rsem (1.3.0)

 path = /Users/Shared/bioinformatics/RSEM-1.3.0

stacks (1.44)

 path = /Users/Shared/bioinformatics/stacks-1.44

tophat (2.1.1)

 path = /Users/Shared/bioinformatics/tophat-2.1.1.OSX_x86_64

trinity (2.3.2)

 path = /Users/Shared/bioinformatics/trinityrnaseq-Trinity-V2.3.2

Computer: emu/roadrunner

OS: Ubuntu 16.04

Bismark (0.16.3)

 path = /home/shared/Bismark

Blasr (5.0.994e5fc)

path = /home/shared/bin/blasr

BSMap (2.90)

 path = /home/shared/bsmap

Comet (2016.01 rev2)

 path = /home/shared/comet/comet.2016012.linux.exe

FastQC (0.11.5)

 path = /home/shared/fastQC/fastqc/

kallisto (0.43.1)

path = /usr/local/bin/kallisto

PB Jelly (15.8.24)

path = /home/shared/PBSuite_15.8.24/bin/Jelly.py

Pecan (?)

 path = /usr/local/bin/pecan

ProteinDigestionSimulator (2.2.6318.19320)

 path = /home/shared/ProtDigSim (note: This only works for the srlab user account)

ReAdW (4.3.1)

 path = /home/shared/ReAdW/ReAdW.2016012.msfilereader.exe

Trim Galore (0.4.2)

 path = /home/shared/trimgalore

XInteract (v5.0, part of the Trans-Proteomic Pipeline)

 path = /usr/tpp_install/tpp/bin/

Computer: Mox (Hyak)

OS: Red Hat Enterprise 7.2 (login nodes)

OS: CentOS Linux 7.2.1511 (build, interactive nodes, & execute nodes)

$/gscratch/srlab/programs
argparse         celera            GATK         MaSuRCA-3.2.3      networkx-1.11  pilon           redundans          smrtanalysis_2.3.0.140936.run     supernova-2.0.0
argparse-1.4.0   decorator-4.0.11  gcc          Metassembler       networkx2      pitchfork       resources          snap                              tmhmm-2.0c
bcl2fastq-v2.20  FastaIndex        get-pip.py   minimap            PBSuite        platanus_1.2.4  samtools-1.4       SOAPdenovo2                       transdecoder
bowtie2-2.1.0    FastQC            git-sym      mummer             pecan          pyScaf          scripts            sqlite                            Trimmomatic-0.36
bwa-0.7.15       gapcloser-1.12    hmmer-3.1b2  MUMmer3.23         perl           quast-4.5       setuptools-36.0.1  SSPACE-LongRead_v1-1              trinity
canu             GARM_v0.7.5       last-852     ncbi-blast-2.6.0+  picard-2.9.1   racon           signalp-4.1        SSPACE-STANDARD-3.0_linux-x86_64  trinotate

Computer: woodpecker

OS: Windows 7 Enterprise (64-bit)

Microsoft Office 2016 Pro Plus

      path = C:\Program Files\Microsoft Office

Protein Digest Simulator v2.2.6138.19320

      path = C:\Program Files (x86)\ProteinDigestionSimulator

Proteowizard v3.0.10577

      path = C:\Program Files\ProteoWizard\ProteoWizard 3.0.10577

Skyline v3.6

      path =

Computer: swan

OS: Windows 7 Enterprise (64-bit)

Microsoft Office Professional 2016 64-bit

  • Access
  • Excel
  • Power Point
  • Word

R v3.4.2

R Studio 1.1383

Skyline v3.7.0.11317

Skyline Daily v3.7.1.11446

Virtual Clonedrive v5.5.0.0

ProteoWizard 3.0.11516 64-bit

  • MSConvert
  • SeeMS

LabX v. 8.0.0 Build 3444

Protein Digest Simulator v2.2.6471; September 19, 2017

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