On Tue, Feb 25, 2014 at 2:29 PM, John Chilton <jmchil...@gmail.com> wrote:
> Hey Peter,
>
> Answers inline.
>
> On Tue, Feb 25, 2014 at 8:08 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>> Hi John,
>>
>> As you noticed (and posted on Twitter), I've just tweaked the NCBI
>> makeblastdb wrapper on GitHub to use a multiple file picker instead
>> of a repeat:
>>
>> https://github.com/peterjc/galaxy_blast/commit/858bf541a828644ea6461b20b687c214b564d3b0
>>
>> That seems to be working fine in human testing (although not on
>> the functional side).
>
> Functional test support for these was added with the latest release
> but only for API driven tests. Can you try adding interactor="api" to
> your test cases?
>
> https://bitbucket.org/galaxy/galaxy-central/commits/211f30207d48101a1250983d4f0f55c937f00a2e

Ah - examples without adding the api flag,

e.g. https://travis-ci.org/peterjc/galaxy_blast/builds/19517715
and https://travis-ci.org/peterjc/galaxy_blast/builds/19570673

Problem where attempts to compare text log file (primary file in
the blast database composite datatype) with a fasta file (see
below).

Suspecting this was due to a change in Galaxy, not the wrapper,
I reran a previously successful TravisCI build from 5 days ago:

https://travis-ci.org/peterjc/galaxy_blast/builds/19248312

This worked - so change to the makeblastdb wrapper changes
seem to be the immediate trigger.

Peter


Snippet from failing test,

AssertionError: History item 1 different than expected, difference (using diff):
( 
/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test-data/four_human_proteins_taxid.fasta.log
v. 
/tmp/tmpNDhPnX/tmpj7U79F/new_files_path_LGtc1w/tmpdBuU0jfour_human_proteins_taxid.fasta.log
)
--- local_file
+++ history_data
@@ -1,10 +1,61 @@
-
-
-Building a new DB, current time: 02/10/2014 18:40:09
-New DB name:   four_human_proteins_taxid.fasta
-New DB title:  Just 4 human proteins
-Sequence type: Protein
-Keep Linkouts: T
-Keep MBits: T
-Maximum file size: 1000000000B
-Adding sequences from FASTA; added 4 sequences in 0.00230002 seconds.
+>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44
OS=Homo sapiens GN=ERP44 PE=1 SV=1
+MHPAVFLSLPDLRCSLLLLVTWVFTPVTTEITSLDTENIDEILNNADVALVNFYADWCRF
+SQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMK
+REYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFER
+VANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDMVYLGAMTNFDVTYNWIQDK
+CVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHAD
+CDKFRHPLLHIQKTPADCPVIAIDSFRHMYVFGDFKDVLIPGKLKQFVFDLHSGKLHREF
+HHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL
+>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens
GN=BMP2K PE=1 SV=2
+MKKFSRMPKSEGGSGGGAAGGGAGGAGAGAGCGSGGSSVGVRVFAVGRHQVTLEESLAEG
+GFSTVFLVRTHGGIRCALKRMYVNNMPDLNVCKREITIMKELSGHKNIVGYLDCAVNSIS
+DNVWEVLILMEYCRAGQVVNQMNKKLQTGFTEPEVLQIFCDTCEAVARLHQCKTPIIHRD
********
*SNIP *
********
+TVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETL
+EIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQE
+RNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQ
+NVTEFDGQDACGSNSWTVVDIDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFS
+DERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDPNGNITHYLVFWE
+RQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQIL
+KELEESSFRKTFEDYLHNVVFVPRKTSSGTGAEDPRPSRKRRSLGDVGNVTVAVPTVAAF
+PNTSSTSVPTSPEEHRPFEKVVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYV
+SARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLCV
+SRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIAKIIIG
+PLIFVFLFSVVIGSIYLFLRKRQPDGPLGPLYASSNPEYLSASDVFPCSVYVPDEWEVSR
+EKITLLRELGQGSFGMVYEGNARDIIKGEAETRVAVKTVNESASLRERIEFLNEASVMKG
+FTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLRSLRPEAENNPGRPPPTLQEMIQMA
+AEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRDIYETDYYRKGGKGLLPV
+RWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDN
+CPERVTDLMRMCWQFNPKMRPTFLEIVNLLKDDLHPSFPEVSFFHSEENKAPESEELEME
+FEDMENVPLDRSSHCQREEAGGRDGGSSLGFKRSYEEHIPYTHMNGGKKNGRILTLPRSN
+PS
+>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
+MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY
+VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG
+GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP
+EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES
+ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI
+YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA

P.S. The extra space in "*SNIP *" got lost in my emailed patch,
https://bitbucket.org/galaxy/galaxy-central/diff/test/base/twilltestcase.py?diff2=15fc8675064e&at=default
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to