Galaxy as an API IDE. (Incredibly insecure but possible)

24 Aug 2012

      Anyone developing API scripts who likes to live dangerously - please read
on.

I just tested and blend-lib api scripts work fine in Galaxy when pasted
into a Tool Factory form. No need to generate a new tool.

Compared with running in a console, you get persistence and other framework
benefits plus at no extra charge, a ginormous security problem if you share
the history or any outputs because they contain the api script with key so
development servers only please!

Leave the input box empty, set the interpreter to python, paste and run an
api script - eg working example (substitute the url and key) below.

Took me a few iterations to develop the example - after each run, the
(edited..) api script is conveniently recreated using the redo button on
the history output item.
So each successive version of the developing api script I ran was persisted
- ready to be edited and rerun easily - handy being able to quickly inspect
dicts to help move progressively deeper iteratively.

Give the below a whirl on a private clone (install the tool factory from
the main toolshed) and try adding complexity with few rerun/edit/rerun
cycles.

=============Eg tool factory api script=======================

import sys
from blend.galaxy import GalaxyInstance
ourGal = 'http://x.x.x.x:xxxx'
ourKey = 'xxx'
gi = GalaxyInstance(ourGal, key=ourKey)
libs = gi.libraries.get_libraries()
res = []
for lib in libs: #u'url': u'/galaxy/api/libraries/441d8112651dc2f3', u'id':
u'441d8112651dc2f3', u'name': u'Demonstration sample RNA data',
    res.append('%s:\n' % lib['name'])
    res.append(str(gi.libraries.show_library(lib['id'],contents=True)))
outf=open(sys.argv[2],'w')
outf.write('\n'.join(res))
outf.close()

returns a history item with:

Demonstration sample RNA data:[{u'url':
u'/galaxy/api/libraries/441d8112651dc2f3/contents/F8de0c7750d06c0d0',
u'type': u'folder', u'name': u'/', u'id': u'F8de0c7750d06c0d0'}, {u'url':
u'/galaxy/api/libraries/441d8112651dc2f3/contents/F7d480bbb847db8d0',
u'type': u'folder', u'name': u'/rnaseq demo data', u'id':
u'F7d480bbb847db8d0'}, {u'url':
u'/galaxy/api/libraries/441d8112651dc2f3/contents/8b25a086f3d48921',
u'type': u'file', u'name': u'/rnaseq demo
data/hg19_exons_mergedGENENAMES.bed', u'id': u'8b25a086f3d48921'}, {u'url':
u'/galaxy/api/libraries/441d8112651dc2f3/contents/5091b660e3557a3e',
u'type': u'file', u'name': u'/rnaseq demo data/Select first on
Ctrl_HAEC_FC078_1_sequence.txt (data 1)', u'id': u'5091b660e3557a3e'},
{u'url':
u'/galaxy/api/libraries/441d8112651dc2f3/contents/4e084a2837e50c40',
u'type': u'file', u'name': u'/rnaseq demo data/Select first on
Ctrl_HAEC_FC078_4_sequence.txt (data 4)', u'id': u'4e084a2837e50c40'},
{u'url':
u'/galaxy/api/libraries/441d8112651dc2f3/contents/0ab9ae3dbe24ad04',
u'type': u'file', u'name': u'/rnaseq demo data/Select first on
Ctrl_HAEC_FC079_1_sequence.txt (data 7)', u'id': u'0ab9ae3dbe24ad04'},
{u'url':
u'/galaxy/api/libraries/441d8112651dc2f3/contents/0a773730795f59a9',
u'type': u'file', u'name': u'/rnaseq demo data/Select first on
HG_HAEC_FC078_2_sequence.txt (data 2)', u'id': u'0a773730795f59a9'},
{u'url':
u'/galaxy/api/libraries/441d8112651dc2f3/contents/c810c4dc5aed60ac',
u'type': u'file', u'name': u'/rnaseq demo data/Select first on
HG_HAEC_FC078_5_sequence.txt (data 5)', u'id': u'c810c4dc5aed60ac'},
{u'url':
u'/galaxy/api/libraries/441d8112651dc2f3/contents/ee5b8d53fd29c05c',
u'type': u'file', u'name': u'/rnaseq demo data/Select first on
HG_HAEC_FC079_2_sequence.txt (data 8)', u'id': u'ee5b8d53fd29c05c'},
{u'url':
u'/galaxy/api/libraries/441d8112651dc2f3/contents/1e04e5f52ca2af6e',
u'type': u'file', u'name': u'/rnaseq demo data/Select first on
HN_HAEC_FC078_3_sequence.txt (data 3)', u'id': u'1e04e5f52ca2af6e'},
{u'url':
u'/galaxy/api/libraries/441d8112651dc2f3/contents/7e05ba393ab04bc6',
u'type': u'file', u'name': u'/rnaseq demo data/Select first on
HN_HAEC_FC078_6_sequence.txt (data 6)', u'id': u'7e05ba393ab04bc6'},
{u'url':
u'/galaxy/api/libraries/441d8112651dc2f3/contents/335753abc7341224',
u'type': u'file', u'name': u'/rnaseq demo data/Select first on
HN_HAEC_FC079_3_sequence.txt (data 9)', u'id': u'335753abc7341224'},
{u'url':
u'/galaxy/api/libraries/441d8112651dc2f3/contents/09c975479974360d',
u'type': u'file', u'name': u'/smalltest.sam', u'id':
u'09c975479974360d'}]Public
data:[{u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/F37c082b4cb3811bd',
u'type': u'folder', u'name': u'/', u'id': u'F37c082b4cb3811bd'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/F5390d290c0aca35b',
u'type': u'folder', u'name': u'/1000 genomes and other public fastq and bam
samples', u'id': u'F5390d290c0aca35b'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/721cc53ac555050e',
u'type': u'file', u'name': u'/1000 genomes and other public fastq and bam
samples/
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA20351/sequence_read/SRR040058.filt.fastq',
u'id': u'721cc53ac555050e'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/a96ce863d2b9a69a',
u'type': u'file', u'name': u'/1000 genomes and other public fastq and bam
samples/
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA20351/sequence_read/SRR040058.filt.fastq(data
10)_FastQC.html', u'id': u'a96ce863d2b9a69a'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/81d4a112e7668435',
u'type': u'file', u'name': u'/1000 genomes and other public fastq and bam
samples/1000g paired sample chr20', u'id': u'81d4a112e7668435'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/00776454b8f394c8',
u'type': u'file', u'name': u'/1000 genomes and other public fastq and bam
samples/1000g chrom 10 single QC sample', u'id': u'00776454b8f394c8'},
{u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/0ff2a12d5b5e045a',
u'type': u'file', u'name': u'/1000 genomes and other public fastq and bam
samples/1000g sample chr1 single ended reads', u'id': u'0ff2a12d5b5e045a'},
{u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/8b394966390e7e29',
u'type': u'file', u'name': u'/1000 genomes and other public fastq and bam
samples/Galaxy_GM12878.fastqillumina', u'id': u'8b394966390e7e29'},
{u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/1b82079d07b4928f',
u'type': u'file', u'name': u'/1000 genomes and other public fastq and bam
samples/Galaxy_GM12878.fastqilluminaFastQC.html', u'id':
u'1b82079d07b4928f'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/F2ef8c0af274c514d',
u'type': u'folder', u'name': u'/BioMart', u'id': u'F2ef8c0af274c514d'},
{u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/F1ba8da1da6710cd5',
u'type': u'folder', u'name': u'/BioMart/RefSeq2GeneName', u'id':
u'F1ba8da1da6710cd5'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/b5e989c148cd0aa1',
u'type': u'file', u'name':
u'/BioMart/RefSeq2GeneName/mm9_Names_RefSeq.txt', u'id':
u'b5e989c148cd0aa1'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/F6cd82b8eed63ee9a',
u'type': u'folder', u'name': u'/encode', u'id': u'F6cd82b8eed63ee9a'},
{u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/F177c1b293cbb701a',
u'type': u'folder', u'name': u'/encode/FAIRE', u'id':
u'F177c1b293cbb701a'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/ee24d81f0dee6a46',
u'type': u'file', u'name': u'/encode/FAIRE/FASTQ Groomer on data 1', u'id':
u'ee24d81f0dee6a46'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/f4209c75ea186d52',
u'type': u'file', u'name':
u'/encode/FAIRE/wgEncodeUncFAIREseqRawDataRep2K562.fastq', u'id':
u'f4209c75ea186d52'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/cca5cab06be4a64c',
u'type': u'file', u'name':
u'/encode/FAIRE/wgEncodeUncFAIREseqRawDataRep2K562.fastq', u'id':
u'cca5cab06be4a64c'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/Fa72f7b1e35fa5a2e',
u'type': u'folder', u'name': u'/EpiDfiles', u'id': u'Fa72f7b1e35fa5a2e'},
{u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/fa29d7e45271edc8',
u'type': u'file', u'name': u'/EpiDfiles/c2.all.v2.5.symbols.gmt', u'id':
u'fa29d7e45271edc8'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/42a6cd9d5e1f6e99',
u'type': u'file', u'name': u'/EpiDfiles/hg18_refSeq_HUGO_TSS.bed', u'id':
u'42a6cd9d5e1f6e99'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/5d3a4056a308beac',
u'type': u'file', u'name': u'/EpiDfiles/msigdb.v2.5.symbols.gmt', u'id':
u'5d3a4056a308beac'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/02f72b1bb3982091',
u'type': u'file', u'name': u'/EpiDfiles/msigdb.v3.0.symbols.gmt', u'id':
u'02f72b1bb3982091'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/F1bae78f62566eb60',
u'type': u'folder', u'name': u'/hg18', u'id': u'F1bae78f62566eb60'},
{u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/d6f2ea9a5a8e9773',
u'type': u'file', u'name': u'/hg18/hg18_all_mrna_refseq_bed', u'id':
u'd6f2ea9a5a8e9773'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/F9f9703d25abcbc83',
u'type': u'folder', u'name': u'/hg19', u'id': u'F9f9703d25abcbc83'},
{u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/100c928820ad6752',
u'type': u'file', u'name': u'/hg19/Aceview acembly all hg19 exons', u'id':
u'100c928820ad6752'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/aa8ad982a2157051',
u'type': u'file', u'name': u'/hg19/Ensemble_Exon.bed', u'id':
u'aa8ad982a2157051'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/9d7f80d7fdcd55af',
u'type': u'file', u'name': u'/hg19/hg19_exons_mergedAnno.bed', u'id':
u'9d7f80d7fdcd55af'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/45d26ffe370a9ca5',
u'type': u'file', u'name': u'/hg19/hg19_exons_merged.bed', u'id':
u'45d26ffe370a9ca5'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/dc7b5adeccaa6f0c',
u'type': u'file', u'name': u'/hg19/hg19_exons_mergedGENENAMES.bed', u'id':
u'dc7b5adeccaa6f0c'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/9ff231da824ea0fd',
u'type': u'file', u'name': u'/hg19/hg19_transcriptome.bed', u'id':
u'9ff231da824ea0fd'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/1cdbace110dad0e6',
u'type': u'file', u'name': u'/hg19/mirbase_wgRNA_tRNA_rnaGene.fa', u'id':
u'1cdbace110dad0e6'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/cc4f723ba6129868',
u'type': u'file', u'name': u'/hg19/RefSeq_Exon.bed', u'id':
u'cc4f723ba6129868'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/2b827a488c9d67ec',
u'type': u'file', u'name': u'/hg19/refseq hg19 exons ', u'id':
u'2b827a488c9d67ec'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/b99c33bfcc32f3f1',
u'type': u'file', u'name': u'/hg19/small_RNA_UCSC_hg19.bed', u'id':
u'b99c33bfcc32f3f1'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/60d6a0a8c6109c87',
u'type': u'file', u'name': u'/hg19/small_RNA_UCSC_hg19.fa', u'id':
u'60d6a0a8c6109c87'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/6050ca6f6d124ba3',
u'type': u'file', u'name': u'/hg19/UCSC_Main_on_Human__rnaGene.bed', u'id':
u'6050ca6f6d124ba3'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/1ec153edf6ce5fdf',
u'type': u'file', u'name': u'/hg19/UCSC Main on Human: tRNAs (genome)',
u'id': u'1ec153edf6ce5fdf'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/ff10de924c7fe628',
u'type': u'file', u'name': u'/hg19/UCSC Main on Human: wgRna (genome)',
u'id': u'ff10de924c7fe628'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/Fc17d8e8ebb367ac9',
u'type': u'folder', u'name': u'/Local workflow text files and headers',
u'id': u'Fc17d8e8ebb367ac9'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/fd6b69cc0d1fc8b4',
u'type': u'file', u'name': u'/Local workflow text files and
headers/jan14_simple_paired_rnaseq_difference_header', u'id':
u'fd6b69cc0d1fc8b4'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/1a901c238e4d5b5b',
u'type': u'file', u'name': u'/Local workflow text files and headers/jan 18
diff analysis header row', u'id': u'1a901c238e4d5b5b'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/Fee71a1e20a0159ed',
u'type': u'folder', u'name': u'/miR data', u'id': u'Fee71a1e20a0159ed'},
{u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/d3714832a57e85b3',
u'type': u'file', u'name': u'/miR data/hairpin.fa', u'id':
u'd3714832a57e85b3'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/b74b3fb65f9ecfaf',
u'type': u'file', u'name': u'/miR data/Homo_sapiens_MB17_hairpin.fa',
u'id': u'b74b3fb65f9ecfaf'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/4c78e63f5b116eeb',
u'type': u'file', u'name': u'/miR data/Homo_sapiens_MB17_mature.fa', u'id':
u'4c78e63f5b116eeb'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/99e66d6213700ab6',
u'type': u'file', u'name': u'/miR data/hsa_miR.bed', u'id':
u'99e66d6213700ab6'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/0c63d5f08b425c56',
u'type': u'file', u'name': u'/miR data/mature.fa', u'id':
u'0c63d5f08b425c56'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/bab337bfb6e020b4',
u'type': u'file', u'name': u'/miR data/mmu_miR.bed', u'id':
u'bab337bfb6e020b4'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/67c137668f28bbee',
u'type': u'file', u'name': u'/miR data/rno_miR.bed', u'id':
u'67c137668f28bbee'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/Fbd711b80d20ca3b9',
u'type': u'folder', u'name': u'/mm9', u'id': u'Fbd711b80d20ca3b9'},
{u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/ed91cb1a2554ec0c',
u'type': u'file', u'name': u'/mm9/mm9_Refmrna.bed', u'id':
u'ed91cb1a2554ec0c'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/143a41beb0a465a1',
u'type': u'file', u'name': u'/mm9/mm9_refgene_exons_amalgamated.bed',
u'id': u'143a41beb0a465a1'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/0e5b50af8b43e426',
u'type': u'file', u'name': u'/mm9/mm9_ENSGENE_exons_amalgamated.bed',
u'id': u'0e5b50af8b43e426'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/4b1a8b3ff49700bd',
u'type': u'file', u'name': u'/mm9/UCSC Main on Mouse: refGene (genome)',
u'id': u'4b1a8b3ff49700bd'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/F2d30dd41a948ff46',
u'type': u'folder', u'name': u'/rn4', u'id': u'F2d30dd41a948ff46'},
{u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/0af450a98016a5bf',
u'type': u'file', u'name': u'/rn4/rn4_refseq.bed', u'id':
u'0af450a98016a5bf'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/23b6b394755cb983',
u'type': u'file', u'name': u'/rn4/rn4.fa', u'id': u'23b6b394755cb983'},
{u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/6eb0dce194a0951b',
u'type': u'file', u'name': u'/rn4/rn4_symbol.bed', u'id':
u'6eb0dce194a0951b'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/Fa7bbd9bf2f387c80',
u'type': u'folder', u'name': u'/rn5', u'id': u'Fa7bbd9bf2f387c80'},
{u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/bc8aacf7d0171089',
u'type': u'file', u'name': u'/rn5/Rattus_norvegicus_hairpin.fa', u'id':
u'bc8aacf7d0171089'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/6e47b270a4c2bd9a',
u'type': u'file', u'name': u'/rn5/Rattus_norvegicus_mature.fa', u'id':
u'6e47b270a4c2bd9a'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/3afff7e53e7e8d39',
u'type': u'file', u'name': u'/rn5/rn5.fa', u'id': u'3afff7e53e7e8d39'},
{u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/f0655257dc41a11e',
u'type': u'file', u'name': u'/rn5/rn5 refGene gtf august 21', u'id':
u'f0655257dc41a11e'}]Sample analyses and demonstration outputs:[{u'url':
u'/galaxy/api/libraries/b318d28ff7462b6a/contents/F50341ab0b3df0ae8',
u'type': u'folder', u'name': u'/', u'id': u'F50341ab0b3df0ae8'}, {u'url':
u'/galaxy/api/libraries/b318d28ff7462b6a/contents/Ffb72a36640097dbe',
u'type': u'folder', u'name': u'/qc demos', u'id': u'Ffb72a36640097dbe'},
{u'url':
u'/galaxy/api/libraries/b318d28ff7462b6a/contents/f5a85862afc5ed23',
u'type': u'file', u'name': u'/qc demos/Draw nucleotides distribution chart
on data 5', u'id': u'f5a85862afc5ed23'}, {u'url':
u'/galaxy/api/libraries/b318d28ff7462b6a/contents/ff852b8d55f36ba4',
u'type': u'file', u'name': u'/qc demos/Draw quality score boxplot on data
5', u'id': u'ff852b8d55f36ba4'}, {u'url':
u'/galaxy/api/libraries/b318d28ff7462b6a/contents/7986d528d5b4a4a3',
u'type': u'file', u'name': u'/qc demos/FastQC demo.html', u'id':
u'7986d528d5b4a4a3'}, {u'url':
u'/galaxy/api/libraries/b318d28ff7462b6a/contents/8332fcb92fd16073',
u'type': u'file', u'name': u'/qc demos/FC052_6_H3K4_me3_mock GC bias
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