The final tool migration?

[martenson]

I think we still have tools in distribution that would profit from being migrated to the TS. What do others think?

e.g.: https://github.com/galaxyproject/galaxy/pull/588

Tools in the distribution which are not data source or text manipulation:

Tool Name	Description	Tool ID	Version	Action
aaChanges	amino-acid changes caused by a set of SNPs	hgv_codingSnps	1.0.0
Aggregate datapoints	Appends the average, min, max of datapoints per interval	aggregate_scores_in_intervals2	1.1.3
AXT to concatenated FASTA	Converts an AXT formatted file to a concatenated FASTA alignment	axt_to_concat_fasta	1.0.0
AXT to FASTA	Converts an AXT formatted file to FASTA format	axt_to_fasta	1.0.0
AXT to LAV	Converts an AXT formatted file to LAV format	axt_to_lav_1	1.0.0
Bar chart	for multiple columns	barchart_gnuplot	1.0.0
BEAM	significant single- and multi-locus SNP associations in case-control studies	hgv_beam	1.0.0
BED-to-bigBed	converter	bed_to_bigBed	1.0.0
BED-to-GFF	converter	bed2gff1	2.0.0
BLAT	compare sequencing reads against UCSC genome builds	blat_wrapper	1.0.0
Boxplot	of quality statistics	qual_stats_boxplot	1.0.0
Compare two Datasets	to find common or distinct rows	comp1	1.0.2
Compute quality statistics	for SOLiD data	solid_qual_stats	1.0.0
Convert genome coordinates	between assemblies and genomes	liftOver1	1.0.4
Convert	SOLiD output to fastq	solid2fastq	1.0.0
Count	occurrences of each record	Count1	1.0.2
Create single interval	as a new dataset	createInterval	1.0.0
DAVID	functional annotation for a list of genes	hgv_david	1.0.1
Draw quality score boxplot	for SOLiD data	solid_qual_boxplot	1.0.0
Extract features	from GFF data	Extract_features1	1.0.0
Extract Genomic DNA	using coordinates from assembled/unassembled genomes	Extract genomic DNA 1	2.2.3
Extract MAF blocks	given a set of genomic intervals	Interval2Maf1	1.0.1
Extract MAF by block number	given a set of block numbers and a MAF file	maf_by_block_number1	1.0.1
Extract Pairwise MAF blocks	given a set of genomic intervals	Interval2Maf_pairwise1	1.0.1
FASTQ Conversions	converts between FASTQ data and other data formats	fastq_conversions	1.0.0
FASTQ Groomer	converts any FASTQ to Sanger	fastq_gen_conv	1.0.0
FASTQ Statistics	for Solexa file	cshl_fastq_statistics	1.0.0
Filter GFF data by attribute	using simple expressions	gff_filter_by_attribute	0.1.1
Filter GFF data by feature count	using simple expressions	gff_filter_by_feature_count	0.1.1
Filter GTF data by attribute values_list	None	gtf_filter_by_attribute_values_list	0.1
Filter MAF blocks	by Size	maf_limit_size1	1.0.1
Filter MAF blocks	by Species	MAF_Limit_To_Species1	1.0.0
Filter MAF	by specified attributes	MAF_filter	1.0.1
FIMO	Find Individual Motif Occurrences	meme_fimo	0.0.1
Find Similarities and Differences	between two datasets	Comm1	1.0.0
g:Profiler	tools for functional profiling of gene lists	hgv_linkToGProfile	1.0.0
Gene BED To Exon/Intron/Codon BED	expander	gene2exon1	1.0.0
Gene BED To Intron BED	expander	gene2intron1	1.0.0
Gene Table To BED	Parse a UCSC Gene Table dump	ucsc_gene_table_to_intervals1	1.0.0
GFF-to-BED	converter	gff2bed1	1.0.1
GPASS	significant single-SNP associations in case-control studies	hgv_gpass	1.0.0
Group	data by a column and perform aggregate operation on other columns.	Grouping1	2.1.1
GTF-to-BEDGraph	converter	gtf2bedgraph	1.0.0
Join MAF blocks	by Species	MAF_Thread_For_Species1	1.0.0
Join two Datasets	side by side on a specified field	join1	2.0.2
LAJ	Pairwise Alignment Viewer	laj_1	1.0.0
LAV to BED	Converts a LAV formatted file to BED format	lav_to_bed1	1.0.0
LD	linkage disequilibrium and tag SNPs	hgv_ldtools	1.0.0
LPS	LASSO-Patternsearch algorithm	hgv_lps	1.0.0
MAF Coverage Stats	Alignment coverage information	maf_stats1	1.0.1
MAF to BED	Converts a MAF formatted file to the BED format	MAF_To_BED1	1.0.0
MAF to FASTA	Converts a MAF formatted file to FASTA format	MAF_To_Fasta1	1.0.1
MAF to Interval	Converts a MAF formatted file to the Interval format	MAF_To_Interval1	1.0.0
Map with BFAST	None	bfast_wrapper	0.1.3
Map with Mosaik	None	mosaik_wrapper	1.1.2
Map with PerM	for SOLiD and Illumina	PerM	1.1.2
MAQ for SOLiD		maq_cs_wrapper	1.0.0
MasterVar to gd_snp	Convert from MasterVar to gd_snp table	master2gd_snp	1.0.0
MasterVar to pgSnp	Convert from MasterVar to pgSnp format	master2pgSnp	1.0.0
Match	a column from one Query against another Query	fileGrep1	1.0.0
MEME	Multiple Em for Motif Elicitation	meme_meme	1.0.0
Merge Columns	together	mergeCols1	1.0.1
PASS	significant transcription factor binding sites from ChIP data	hgv_pass	1.0.0
phyloP	interspecies conservation scores	hgv_add_scores	1.0.0
Re-align with SRMA	None	srma_wrapper	0.2.5
Relational join 2	two datasets a specific column of which has the same value	joiner2	1.0.0
Reverse Complement	a MAF file	MAF_Reverse_Complement_1	1.0.1
Secure Hash / Message Digest	on a dataset	secure_hash_message_digest	0.0.1
SFF converter	None	Sff_extractor	1.0.1
SHRiMP for Color-space	reads mapping against reference sequence	shrimp_color_wrapper	1.0.0
SHRiMP for Letter-space	reads mapping against reference sequence	shrimp_wrapper	1.0.0
SIFT	predictions of functional sites	hgv_sift	1.0.0
Simulate	Illumina runs	ngs_simulation	1.0.0
SOLiD-to-FASTQ	converts SOLiD data to FASTQ data	solid_to_fastq	1.0.0
Split MAF blocks	by Species	MAF_split_blocks_by_species1	1.0.0
Stitch Gene blocks	given a set of coding exon intervals	GeneBed_Maf_Fasta2	1.0.1
Stitch MAF blocks	given a set of genomic intervals	Interval_Maf_Merged_Fasta2	1.0.1
Summary Statistics	for any numerical column	Summary_Statistics1	1.1.1
VCF to MAF Custom Track	for display at UCSC	vcf_to_maf_customtrack1	1.0.0
velvetg	Velvet sequence assembler for very short reads	velvetg	1.0.0
velveth	Prepare a dataset for the Velvet velvetg Assembler	velveth	1.0.0
Wig/BedGraph-to-bigWig	converter	wig_to_bigWig	1.1.0
Wiggle-to-Interval	converter	wiggle2simple1	1.0.0

[davebx]

:+1: For migrating some tools.

[blankenberg]

Sounds good to me. We should of course test and verify the migration scripts, etc. Also, we should start a list of tools to migrate.

[bgruening]

:+1: for starting a list of tools and the migration. I would not rush with this and try to get it into the next release. Imho this should be the last migration ever. Migrations can be painful.

[martenson]

Afaik the requirements for migration are:

• to not migrate text-manipulation tools
• migration should not take unreasonably long (~10min fine?) anything else?

I hope we can make this the final migration.

@bgruening I also feel no rush - removed release from title.

[jmchilton]

I would recommend planning to do this someday but not spending time on it right now, doesn't seem important to me with everything in flux.

[hexylena]

Agreed with @jmchilton

Also xref #361

[martenson]

a tool that needs to be migrated for https://github.com/galaxyproject/tools-iuc/issues/404 is https://toolshed.g2.bx.psu.edu/view/iuc/extract_genomic_dna/702970e4a134