Re: Request for sponsorship: ruby-crb-blast

2018-04-24 Thread Chris Hofstaedtler 
* Michael Crusoe  [180413 15:54]:
> 2018-04-13 16:00 GMT+03:00 Chris Hofstaedtler :
> 
[...]
> >
> >   Error: Argument "num_threads". Illegal value, expected (>=1 and
> > =<4):  `6'
> >   Error:  (CArgException::eConstraint) Argument "num_threads". Illegal
> > value, expected (>=1 and =<4):  `6'
> > /<>/debian/ruby-crb-blast/usr/lib/ruby/vendor_
> > ruby/crb-blast/crb-blast.rb:214:in `run_blast_with_threads'
> > /<>/debian/ruby-crb-blast/usr/lib/ruby/vendor_
> > ruby/crb-blast/crb-blast.rb:173:in `run_blast'
> >
> > I assume this is caused by your fewer-threads patch :)
> >
> 
> Strange, this behaviour is explictly fixed by
> https://salsa.debian.org/ruby-team/ruby-crb-blast/blob/master/debian/patches/test_less_threads
> Looks like I missed a couple other examples, so I pushed another commit.
> Does that fix it for you?

Sorry, was busy with other stuff.

It indeed does fix it.

I've uploaded this now and moved the tag.

Please fix these for the next revision though:

W: ruby-crb-blast source: vcs-deprecated-in-debian-infrastructure vcs-browser 
https://anonscm.debian.org/cgit/pkg-ruby-extras/ruby-crb-blast.git
W: ruby-crb-blast source: vcs-deprecated-in-debian-infrastructure vcs-git 
https://anonscm.debian.org/git/pkg-ruby-extras/ruby-crb-blast.git

Chris

Re: Request for sponsorship: ruby-crb-blast

2018-04-13 Thread Lucas Kanashiro 
Hi,


On 04/13/2018 10:36 AM, Michael Crusoe wrote:
>
> 2018-04-13 16:00 GMT+03:00 Chris Hofstaedtler  >:
>
> * Michael Crusoe  > [180413 14:30]:
> > Due to a bug the binary package was deleted in unstable which is 
> blocking
> > me as a DM from uploading the new version:
>
> Had a quick look, but on my 4-core machine the tests are failing,
> snippet of one:
>
>
> Thanks for checking!
>  
>
>
>       test: crb-blast should not find fake scaffold name. :     E
>    
> 
> ===
>     Error: test: crb-blast should not find fake scaffold name.
> (TestCRBBlast):
>       RuntimeError: BLAST Error:
>       USAGE
>         blastx [-h] [-help] [-import_search_strategy filename]
>           [-export_search_strategy filename] [-task task_name]
> [-db database_name]
>           [-dbsize num_letters] [-gilist filename] [-seqidlist
> filename]
>           [-negative_gilist filename] [-negative_seqidlist filename]
>           [-entrez_query entrez_query] [-db_soft_mask
> filtering_algorithm]
>           [-db_hard_mask filtering_algorithm] [-subject
> subject_input_file]
>           [-subject_loc range] [-query input_file] [-out output_file]
>           [-evalue evalue] [-word_size int_value] [-gapopen
> open_penalty]
>           [-gapextend extend_penalty] [-qcov_hsp_perc float_value]
>           [-max_hsps int_value] [-xdrop_ungap float_value]
> [-xdrop_gap float_value]
>           [-xdrop_gap_final float_value] [-searchsp int_value]
>           [-sum_stats bool_value] [-max_intron_length length]
> [-seg SEG_options]
>           [-soft_masking soft_masking] [-matrix matrix_name]
>           [-threshold float_value] [-culling_limit int_value]
>           [-best_hit_overhang float_value] [-best_hit_score_edge
> float_value]
>           [-window_size int_value] [-ungapped] [-lcase_masking]
> [-query_loc range]
>           [-strand strand] [-parse_deflines] [-query_gencode
> int_value]
>           [-outfmt format] [-show_gis] [-num_descriptions int_value]
>           [-num_alignments int_value] [-line_length line_length]
> [-html]
>           [-max_target_seqs num_sequences] [-num_threads
> int_value] [-remote]
>           [-comp_based_stats compo] [-use_sw_tback] [-version]
>
>       DESCRIPTION
>          Translated Query-Protein Subject BLAST 2.7.1+
>
>       Use '-help' to print detailed descriptions of command line
> arguments
>      
> 
>
>       Error: Argument "num_threads". Illegal value, expected (>=1
> and =<4):  `6'
>       Error:  (CArgException::eConstraint) Argument "num_threads".
> Illegal value, expected (>=1 and =<4):  `6'
>    
> 
> /<>/debian/ruby-crb-blast/usr/lib/ruby/vendor_ruby/crb-blast/crb-blast.rb:214:in
> `run_blast_with_threads'
>    
> 
> /<>/debian/ruby-crb-blast/usr/lib/ruby/vendor_ruby/crb-blast/crb-blast.rb:173:in
> `run_blast'
>
> I assume this is caused by your fewer-threads patch :)
>
>
> Strange, this behaviour is explictly fixed
> by 
> https://salsa.debian.org/ruby-team/ruby-crb-blast/blob/master/debian/patches/test_less_threads
> Looks like I missed a couple other examples, so I pushed another
> commit. Does that fix it for you?
>  

FYI, my machine has 4 cores and the tests are passing here.

Cheers.






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Re: Request for sponsorship: ruby-crb-blast

2018-04-13 Thread Michael Crusoe 
2018-04-13 16:00 GMT+03:00 Chris Hofstaedtler :

> * Michael Crusoe  [180413 14:30]:
> > Due to a bug the binary package was deleted in unstable which is blocking
> > me as a DM from uploading the new version:
>
> Had a quick look, but on my 4-core machine the tests are failing,
> snippet of one:
>

Thanks for checking!


>
>   test: crb-blast should not find fake scaffold name. : E
> 
> ===
> Error: test: crb-blast should not find fake scaffold name.
> (TestCRBBlast):
>   RuntimeError: BLAST Error:
>   USAGE
> blastx [-h] [-help] [-import_search_strategy filename]
>   [-export_search_strategy filename] [-task task_name] [-db
> database_name]
>   [-dbsize num_letters] [-gilist filename] [-seqidlist filename]
>   [-negative_gilist filename] [-negative_seqidlist filename]
>   [-entrez_query entrez_query] [-db_soft_mask filtering_algorithm]
>   [-db_hard_mask filtering_algorithm] [-subject subject_input_file]
>   [-subject_loc range] [-query input_file] [-out output_file]
>   [-evalue evalue] [-word_size int_value] [-gapopen open_penalty]
>   [-gapextend extend_penalty] [-qcov_hsp_perc float_value]
>   [-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap
> float_value]
>   [-xdrop_gap_final float_value] [-searchsp int_value]
>   [-sum_stats bool_value] [-max_intron_length length] [-seg
> SEG_options]
>   [-soft_masking soft_masking] [-matrix matrix_name]
>   [-threshold float_value] [-culling_limit int_value]
>   [-best_hit_overhang float_value] [-best_hit_score_edge
> float_value]
>   [-window_size int_value] [-ungapped] [-lcase_masking]
> [-query_loc range]
>   [-strand strand] [-parse_deflines] [-query_gencode int_value]
>   [-outfmt format] [-show_gis] [-num_descriptions int_value]
>   [-num_alignments int_value] [-line_length line_length] [-html]
>   [-max_target_seqs num_sequences] [-num_threads int_value]
> [-remote]
>   [-comp_based_stats compo] [-use_sw_tback] [-version]
>
>   DESCRIPTION
>  Translated Query-Protein Subject BLAST 2.7.1+
>
>   Use '-help' to print detailed descriptions of command line arguments
>   
> 
>
>   Error: Argument "num_threads". Illegal value, expected (>=1 and
> =<4):  `6'
>   Error:  (CArgException::eConstraint) Argument "num_threads". Illegal
> value, expected (>=1 and =<4):  `6'
> /<>/debian/ruby-crb-blast/usr/lib/ruby/vendor_
> ruby/crb-blast/crb-blast.rb:214:in `run_blast_with_threads'
> /<>/debian/ruby-crb-blast/usr/lib/ruby/vendor_
> ruby/crb-blast/crb-blast.rb:173:in `run_blast'
>
> I assume this is caused by your fewer-threads patch :)
>

Strange, this behaviour is explictly fixed by
https://salsa.debian.org/ruby-team/ruby-crb-blast/blob/master/debian/patches/test_less_threads
Looks like I missed a couple other examples, so I pushed another commit.
Does that fix it for you?


>
> Chris
>
>


-- 
Michael R. Crusoe
Co-founder & Lead, Common Workflow Language project

Direktorius, VšĮ "Darbo eigos", Vilnius, Lithuania
https://orcid.org/-0002-2961-9670

m...@commonwl.org
+1 480 627 9108

Re: Request for sponsorship: ruby-crb-blast

2018-04-13 Thread Chris Hofstaedtler 
* Michael Crusoe  [180413 14:30]:
> Due to a bug the binary package was deleted in unstable which is blocking
> me as a DM from uploading the new version:

Had a quick look, but on my 4-core machine the tests are failing,
snippet of one:

  test: crb-blast should not find fake scaffold name. : E

===
Error: test: crb-blast should not find fake scaffold name. (TestCRBBlast):
  RuntimeError: BLAST Error:
  USAGE
blastx [-h] [-help] [-import_search_strategy filename]
  [-export_search_strategy filename] [-task task_name] [-db 
database_name]
  [-dbsize num_letters] [-gilist filename] [-seqidlist filename]
  [-negative_gilist filename] [-negative_seqidlist filename]
  [-entrez_query entrez_query] [-db_soft_mask filtering_algorithm]
  [-db_hard_mask filtering_algorithm] [-subject subject_input_file]
  [-subject_loc range] [-query input_file] [-out output_file]
  [-evalue evalue] [-word_size int_value] [-gapopen open_penalty]
  [-gapextend extend_penalty] [-qcov_hsp_perc float_value]
  [-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap 
float_value]
  [-xdrop_gap_final float_value] [-searchsp int_value]
  [-sum_stats bool_value] [-max_intron_length length] [-seg SEG_options]
  [-soft_masking soft_masking] [-matrix matrix_name]
  [-threshold float_value] [-culling_limit int_value]
  [-best_hit_overhang float_value] [-best_hit_score_edge float_value]
  [-window_size int_value] [-ungapped] [-lcase_masking] [-query_loc 
range]
  [-strand strand] [-parse_deflines] [-query_gencode int_value]
  [-outfmt format] [-show_gis] [-num_descriptions int_value]
  [-num_alignments int_value] [-line_length line_length] [-html]
  [-max_target_seqs num_sequences] [-num_threads int_value] [-remote]
  [-comp_based_stats compo] [-use_sw_tback] [-version]
  
  DESCRIPTION
 Translated Query-Protein Subject BLAST 2.7.1+
  
  Use '-help' to print detailed descriptions of command line arguments
  
  
  Error: Argument "num_threads". Illegal value, expected (>=1 and =<4):  `6'
  Error:  (CArgException::eConstraint) Argument "num_threads". Illegal 
value, expected (>=1 and =<4):  `6'

/<>/debian/ruby-crb-blast/usr/lib/ruby/vendor_ruby/crb-blast/crb-blast.rb:214:in
 `run_blast_with_threads'

/<>/debian/ruby-crb-blast/usr/lib/ruby/vendor_ruby/crb-blast/crb-blast.rb:173:in
 `run_blast'

I assume this is caused by your fewer-threads patch :)

Chris