I have a very bizarre problem with Galaxy.
I have to run a workflow through the API, since Galaxy cannot deal with many pair-end FASTQ files...
In the past I had no issues with this and it always run as expected.
But in the last few days when I select 2 FASTQ files to be run in with the API, invariably Galaxy chooses a completely different set of files to run the workflow on...
I double checked that I find the right file throug the API and that the ID's are correct and that those ID's are indeed pointing to the right files, but once I pass the MAP to Galaxy, it randomly chooses some file...
Not sure how to test this further..(Using the latest pull from galaxy_central, database @101)
Getting GALAXY configuration settings...
Found FASTQ library: ONCOMED_TEST
Found Workflow: MUT190-1 PE DNA_SEQ - Trimmomatic-BWA-REALIGN-DEDUP-VCF (GRCh37-DECOY)
Found history prefix: ONCOMED-BAKEOFF
Found Galaxy URL: http://srp106:8080/api
[OK]
------------------------------------------------------------------- DISPLAY.py output for the two files I want to run...But different files were run in the WF -----------------------
Getting FASTQ files from the library...
{'/2_181_3_CTTGTA_R1.fastq': '11049d6355c1fae6', '/2_181_3_CTTGTA_R2.fastq': '2172873b78ef3de8'}
[OK] Found 2 FASTQ files
-------------------------------------------------------------------
Retrieving workflow step definitions...
TARGETS (GATK) -> ONCOMED/Baits and Targets/SS_OM_v1_targetsOM.gatk-interval
[OK]
BAITS -> ONCOMED/Baits and Targets/SS_OM_v1_baitsOM.interval
[OK]
COSMIC Dataset -> Annotations/CosmicMutantExport_v56_151111.vcf
[OK]
Mills_and_1000G_gold_standard -> Annotations/Annotations used in GATK-1.5/Mills_and_1000G_gold_standard.indels.b37.sites.vcf
[OK]
Adapters File -> Annotations/Adapters.fasta
[OK]
TARGETS -> ONCOMED/Baits and Targets/SS_OM_v1_targetsOM.interval
[OK]
dbSNP VCF File -> Annotations/Annotations used in GATK-1.5/dbsnp_135.b37.vcf
[OK]
TARGETS400 (GATK) -> ONCOMED/Baits and Targets/SS_OM_v1_targetsOM_PLUS400.gatk-interval
[OK]
-------------------------------------------------------------------
Preparing workflow for :
/2_181_3_CTTGTA_R1.fastq
Response
--------
{'outputs': ['685cc0daf312e1e2', '5faa831fd7938831', '31b4c60b45b51900', '55dec7d4d8038078', '8b4bd251f4acfdb2', '991643c8bf045bdf', '45509d1f3c223d75', '69ee8e65832b0a48', '1d42f64460defe7a', 'c58ddab89b2bb805', '8bfc64bb47770912', 'f204dc7bb5ecfc2e', 'cde9aa04cfe839d1', '6362db4d5959d831', 'c01d9ed9facb9b70', '8a6baaaff54e1b05', '3842cee51a54bc8a', 'a1c8e68fee33b3f4', '7780674a8a538878', '32baf3117f18f4a9', 'd81e438f0fefa4fe', '37291cf3d6fd439a', '9b0ffea8ff1d4477', '8be5b6d3aeb85faf', 'b7c76befdaa37432', 'ffcf2e98e3761238', '900232bec5f8fcbe', 'acb2c56b985cec44', '7f15aaa8ca46161f', 'bb8f19f6facd93af', 'f9c244896d5b57dc', '8512f4fc5aed6ea7', '3f52c44d599b9716', '55806ff905fd6286', '0cb88461cff7d031', 'a273ec073a5ae9a6', 'b4fecb3654146377', '9931773a693bd74d', 'da97567b301b6e88', 'db19f117b9ba1f38', '6e9cefcf946aa2eb', '32b7a1d98d5ba938', '950b17b0eeebc8ce', 'c46ef25bdd0b128c', 'd2d71b57d04fdf56', '99ad472ce159d2b4', 'c2a0592a7bfde32d', 'cd476a668e76e2fd', '610abd782fd87335', 'f65cfa41776c8092', '33a09f65ad37eefb', '6a4013fe7480be2e', '0161b00ac62dd980', '177fef443e7d000a', '093d5543780988ae', '603db5a5490d658a', '5e639ad0ecdbbfaa', '601406f579c6cccc', '318bdcc79e1698f5', '9e0a3f75c768292a', '4a913b7f86293e50', '0edd411e46492187', '270afa41507f14e5', '4b75e21d1ac0d2ad', '1816e3ba5ffa42d6', '71b643cde9fb710c', '62d1d0058327a5da', '133576f2dda5c2b4', '450c3dc15a3aa0a0', '5e747c660af21e40', '7db0323336d28301', '9878576367d5f544', 'b150a412957324a5', 'e97867c104e59e02', 'c8e9faf4b8a01e67', '5d194649d99822eb'], 'history': '31d04ac4a1e13563'}
Member Information
------------------
ldda_id: ccfcc222604b2175
misc_blurb: 14.3 Gb
name: 2_181_3_CTTGTA_R2.fastq
data_type: fastq
file_name: /mnt/ngs/data/ProcessedData/Casava_builds/SEQUENCER02/120608_SN402_0181_AD143FACXX/fastq/2_181_3_CTTGTA_R2.fastq
uploaded_by: tdeboer@genomichealth.com
metadata_sequences: None
template_data: {}
genome_build: hg19-decoy
model_class: LibraryDataset
misc_info: uploaded fastq file
file_size: 15361395563
metadata_data_lines: None
message:
id: 2172873b78ef3de8
date_uploaded: 2012-06-21T17:37:20.383314
metadata_dbkey: hg19-decoy
(galaxy_env)[tdeboer@srp106 api]$ myDisplay.py libraries/fb85969571388350/contents/11049d6355c1fae6
Member Information
------------------
ldda_id: 6768e90755e11e63
misc_blurb: 14.3 Gb
name: 2_181_3_CTTGTA_R1.fastq
data_type: fastq
file_name: /mnt/ngs/data/ProcessedData/Casava_builds/SEQUENCER02/120608_SN402_0181_AD143FACXX/fastq/2_181_3_CTTGTA_R1.fastq
uploaded_by: tdeboer@genomichealth.com
metadata_sequences: None
template_data: {}
genome_build: hg19-decoy
model_class: LibraryDataset
misc_info: uploaded fastq file
file_size: 15361395563
metadata_data_lines: None
message:
id: 11049d6355c1fae6
date_uploaded: 2012-06-21T17:37:19.122245
metadata_dbkey: hg19-decoy