[Iplant-api-dev] List of public application keys

[Matthew Vaughn]

Dear developers,

Please find enclosed a list of public application keys generated from your published applications in the Foundation API. Please review this list, looking for your application, and let me know if I have missed any. Your non-public app versions will still work for you - the publication process involves cloning the existing app, moving that clone's ownership to the iPlant administrative user, and archiving all the dependencies, etc. Your app will not, however, be available to anyone you have not specifically shared with any longer. The 'public' and 'world' ACLs are deprecated in the current release of the API services.

The DE team and I are working on a solution to update your DE apps in place without a need on your part to republish them. If you wish to have us do it for you this time, please send me your OLD appid by Monday.

Cheers,

Matt

Public	ClustalW2-2.1u1	Multiple alignment of nucleic acid and protein sequences
Public	Muscle-3.8.31u1	Multiple sequence alignment by log-expectation
Public	abyss-lonestar-1.3.3u1	ABySS is a de novo, parallel, paired-end sequence assembler
Public	abyss-param-complex-ranger-1.2.7u1	ABySS is a de novo, parallel, paired-end sequence assembler
Public	autodock_vina-1.00u1	AutoDock Vina is a new open-source program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use.
Public	bismark-0.7.4u1	bismark Bisulfite Mapper
Public	bismark_genome_preparation-0.7.4u1	bismark genome preparation
Public	bismark_methylation_extractor-0.7.4u1	bismark methylation extractor
Public	blastx-ranger-2.26u1	Wrapper for 16-core BLASTX on TACC Ranger. Intended for metagenome analysis.
Public	blastx-ranger-ncbi-db-2.2.26u1	High-throughput BLASTX on TACC Ranger
Public	bwa-lonestar-0.5.9u1	bwa 0.5.9 is a next gen sequence aligner
Public	bx_evaluate-1.0.0u1	Summarize 'final-out/results' file from bx_refseq_pipeline.
Public	bx_refseq_pipeline-1.0.0u1	Annotate contigs using the plant RefSeq database
Public	clustalw-ranger-1.0u1	ClustalW 2.1
Public	clustalw2-lonestar-2.1u2	Multiple alignment of nucleic acid and protein sequences
Public	dnalc-cuffdiff-lonestar-2.0.2u1	Find significant changes in transcript expression, splicing, and promoter use.
Public	dnalc-cuffdiff-lonestar-2.0.2u1	Find significant changes in transcript expression, splicing, and promoter use.
Public	dnalc-cufflinks-lonestar-2.0.2u1	Transcript assembly and basic quantitation for RNA-Seq
Public	dnalc-tophat-lonestart-2.0.4u1	A spliced read mapper for RNA-Seq
Public	fasttree-ranger-2.1.4u2	FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.
Public	gatk-1000bulls-geno-lonestar-1.00u1	
Public	grep-ranger-1.0u1	print lines matching a pattern
Public	head-5.97u1	Extract first lines or bytes from a file
Public	head-trestles-5.97u1	Extract first lines or bytes from a file
Public	mafft-lonestar-6.864u1	Multiple alignment program for amino acid or nucleotide sequences
Public	metagenemark-1.00u2	An algorithm for accurate ab initio gene prediction in DNA sequences derived from shotgun sequencing of microbial communities.
Public	muscle-lonestar-3.8.31u2	Multiple sequence alignment by log-expectation
Public	muscle-ranger-2.0u2	MUSCLE: Multiple sequence comparison by log-expectation
Public	newbler-2.6.0u1	Newbler, genome assembler
Public	oases-0.2.08u1	Oases, the transcript assembler
Public	phylip-dna-parsimony-lonestar-3.69u1	DNAPARS
Public	phylip-dna-parsimony-lonestar-3.69u2	DNAPARS
Public	phylip-protein-parsimony-lonestar-3.69u1	PROTPARS
Public	phylip-protein-parsimony-lonestar-3.69u2	PROTPARS
Public	quicktree-dm-lonestar-1.1u1	Neighbour-Joining trees of protein sequences (Distance matrix output)
Public	quicktree-dm-lonestar-1.1u2	Neighbour-Joining trees of protein sequences (Distance matrix output)
Public	quicktree-tree-lonestar-1.1u1	Neighbour-Joining trees of protein sequences (Tree output)
Public	quicktree-tree-lonestar-1.1u2	Neighbour-Joining trees of protein sequences (Tree output)
Public	quline-lonestar-3-0.11u1	QU-GENE does simulations
Public	raxml-lonestar-7.2.8u1	Randomized Axelerated Maximum Likelihood
Public	scarf-1.00u1	A next-gen sequence assembly tool for evolutionary genomics. Designed especially for assembling 454 EST sequences against high quality reference sequences from related species.
Public	soapdenovo-1.05u1	Soapdenovo, genome assembler
Public	trinity_r2012-03-17_lonestar4-1.00u1	Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data
Public	velvetg-1.2.07u1	Velvetg, second step of genome assembly
Public	velveth-1.2.07u1	Velveth, first step of genome assembly
Public	wc-1.00u1	Count words in a file




--
Matthew W. Vaughn, Ph.D.,
Manager, Life Sciences Computing Group
Texas Advanced Computing Center
Austin, TX
vaughn at tacc.utexas.edu | (949) 436-6642