NGS: Software Suites
Ensembl-API
GCATemplates available: no
The Ensembl API is available by loading the following modules:
module load ensembl/94-GCCcore-6.3.0-Perl-5.24.0
module load ensembl-io/94-GCCcore-6.3.0-Perl-5.24.0
module load ensembl-compara/94-GCCcore-6.3.0-Perl-5.24.0
module load ensembl-funcgen/94-GCCcore-6.3.0-Perl-5.24.0
module load ensembl-variation/94-GCCcore-6.3.0-Perl-5.24.0
See the Ensembl Core API Tutorial for usage.
EMBOSS
GCATemplates available: no
module spider EMBOSS
EMBOSS homepage
UCSCtools
GCATemplates available: no
List of tools and usages found here
module spider UCSCtools
DART
GCATemplates available: no
DART homepage
module spider DART
For DART applications requiring Java, Perl or Python, you will need to load an appropriate version that matches the DART goolf toolchain:
module load Java/1.8.0_66
module load Python/2.7.10-goolf-1.7.20
module load Perl/5.20.0-goolf-1.7.20
The DART library includes a number of bioinformatics programs, including: stemloc for RNA alignment; xrate for phylo-grammars; phylocomposer, handalign and other statistical alignment programs in the Handel package; and more.
The programs use statistical algorithms (MCMC, EM, etc.) to impute multiple alignments, annotations and other unseen evolutionary parameters from sequence data.
PLINK
GCATemplates available: no
PLINK homepage
module spider PLINK
PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
PLINK 1.9
Plink v1.9 is still beta and being updated frequently so it is best not to add to the HPRC clusters as a module.
There is a precompiled Linux 64-bit (Stable (beta 6.8, 15 Feb) or newer) binary version available that you can download and add to your $PATH.
Version 1.9 will change frequently since it is still beta so you should review your results files and check their website and download the latest version as needed.
Gemini
GCATemplates available: no
Gemini homepage
module spider Gemini
GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome.
Gemini Data is saved here:
/scratch/datasets/Gemini
GenHub
GCATemplates available: no
GenHub homepage
GenHub is a free open-source software framework for analyzing eukaryotic genomes, computing and reporting a variety of statistics reflecting genome content and organization.
module load GenomeTools/1.5.9-intel-2015B
module load AEGeAn/0.15.2-intel-2015B
module load CD-HIT/4.6.6-intel-2015B
module load pandas/0.17.0-intel-2015B-Python-2.7.10
module swap Python python/2.7.6-generic
CGAT
CGAT homepage
Use the following command to find a CGAT version to load using the 'module load' command
module spider CGAT
CGAT is a collection of tools for the computational genomicist written in the python language.
To use CGAT you need to load the CGAT environment:
source $CGAT_ACTIVATE cgat-scripts
When your processing is finished, you need to unload the CGAT environment:
source deactivate
The following CGAT tools are available in the CGAT package
gff2bed
bam2bam chain2psl gff2coverage
bam2bed chain2stats gff2fasta
bam2fastq diff_bam gff2gff
bam2geneprofile diff_bed gff2histogram
bam2peakshape diff_chains gff2psl
bam2stats diff_fasta gff2stats
bam2wiggle diff_gtf gtf2fasta
bam_vs_bam fasta2bed gtf2gff
bam_vs_bed fasta2fasta gtf2gtf
bam_vs_gtf fasta2kmercontent gtf2table
bed2bed fasta2table gtf2tsv
bed2fasta fasta2variants gtfs2tsv
bed2gff fastas2fasta index_fasta
bed2stats fastq2fastq split_gff
bed2table fastq2table vcf2vcf
beds2beds fastqs2fasta version
beds2counts fastqs2fastqs
with user(s) on the same Galaxy instance
User with History to share:
Click 'History options' -> 'Share or Publish'
Select "Share with another user" and enter the Galaxy users full email address.
User receiving shared history:
Click 'History options' -> 'Histories Shared with Me'
Check the box for the history you want to copy to your list of Histories and click Copy.
Then click the 'View all Histories' icon in the right panel to see the shared history in your list of histories.
Manage your HPRC Accounts
There are a number of different types of tools that are configured to require different amounts of SUs.
Here is how SUs are calculated:
Max runtime Cores Calculation Required SUs
1 day 1 24 hrs * 1 day * 1 core = 48
1 day 48 24 hrs * 1 day * 48 cores = 1152
3 days 48 24 hrs * 3 days * 48 cores = 3456
7 days 48 24 hrs * 7 days * 48 cores = 8064
If a tool does not state how many SUs it requires, then it is most likely configured to use 1 core for 1 day (24 SUs). If you are unsure of how many SUs the tool requires, run your "My HPRC SU balance" tool before you submit a job and then run it again after the job starts running. You will be able to see how many SUs were charged to your account.
Using the following HPRC SU balance as an example, if you have two accounts and one is configured as the default (as indicated by Y in the default column), the SUs will only be taken from the account with Y in the Default column:
Starting balance example:
=====================================================================
List of users's Project Accounts
---------------------------------------------------------------------
| Account | Default | Allocation |Used & Pending SUs| Balance |
---------------------------------------------------------------------
|000000000001| Y| 5000.00| 0.00| 5000.00|
|000000000002| N| 5000.00| 0.00| 5000.00|
---------------------------------------------------------------------
After submitting a job that requires 1440 SUs and the job starts running, your balance will look like this:
=====================================================================
List of users's Project Accounts
---------------------------------------------------------------------
| Account | Default | Allocation |Used & Pending SUs| Balance |
---------------------------------------------------------------------
|000000000001| Y| 5000.00| -1440.00| 3560.00|
|000000000002| N| 5000.00| 0.00| 5000.00|
---------------------------------------------------------------------
Now if you submit two more jobs that require 1440 SUs, then your balance will look like this once the jobs start running
=====================================================================
List of users's Project Accounts
---------------------------------------------------------------------
| Account | Default | Allocation |Used & Pending SUs| Balance |
---------------------------------------------------------------------
|000000000001| Y| 5000.00| -4320.00| 680.00|
|000000000002| N| 5000.00| 0.00| 5000.00|
---------------------------------------------------------------------
Now you should not submit any more jobs that require 1440 SUs since your default account only has 680 SUs.
If you need to submit more 1440 SU jobs, then you will need to change your default account to your other account that has a balance of 5000 SUs.
If you do not change your default and try to submit a 1440 SU job and you only have 680 SUs in your default account, then your job will remain in a queued state and will never run. It will get stopped if Galaxy is restarted but otherwise, you will have to stop the job.
If your three 1440 SU jobs complete early, after 1 day for example, then you will be reimbursed for the unused 2 days (960 SUs per job) for each of the three jobs and your HPRC SU balance will look like this:
=====================================================================
List of users's Project Accounts
---------------------------------------------------------------------
| Account | Default | Allocation |Used & Pending SUs| Balance |
---------------------------------------------------------------------
|000000000001| Y| 5000.00| -1440.00| 3560.00|
|000000000002| N| 5000.00| 0.00| 5000.00|
---------------------------------------------------------------------
You can now use the default account if you want to run a job that requires 1440 SUs since the balance has increased to greater than 1440 SUs.