gzipped FASTA input support #102
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Cross reference #98, I will merge that now. |
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This includes support for gzip'ed FASTA input - see #101 |
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Judging from the cron jobs, the failing TravisCI tests on the master are in part upstream changes and/or other issues with the dependencies stack. Sigh. |
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@peterjc please take a look at makeblastdb |
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@nekrut I'm hoping to pull in your changes by hand (keeping authorship intact), and ought to be able to test locally even if TravisCI is giving me trouble. Thanks for working on this. See also galaxyproject/galaxy#6180 which is one of the issues at play. |
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@peterjc I don't care about the authorship as long as things work, so do whatever is easiest |
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Maintaining git authorship is simple enough, I just need to get my master branch tests working again... #103 seems to have fixed testing with the Galaxy dev branch :) |
See pull request peterjc#102
See pull request peterjc#102
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Rebased, squashed a few commits, removed the change to the version scheme, and updated the README. Let's see if TravisCI is happy, then think about adding tests for building databases from gzipped FASTA files. I note that as written this adds additional dependencies on the magic library... |
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The TIGRFAM URL seems to be causing more trouble, see also https://twitter.com/pjacock/status/998941086168076288 and d31e21d |
Also wrap tokens in Cheetah with braces, and more quoting of arguments in the command line.
This is to simplify deployment, especially on older Galaxy installations which are not yet using conda. This was tested under both Python 2 and 3.
This is several command line arguments in one token.
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Still a couple of tests failing, We need to update |
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That took a while - does this look OK now to merge from your point of view @nekrut? Thanks! |
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If I don't hear otherwise this week, I aim to merge this. The main gotcha (which the test suite caught) was reverting some of the quoting of arguments in the wrapper (normally good practise in Galaxy wrappers, but here can't be used in a couple of cases where a UI option is mapped to multiple command line switches). |
| @ADV_FILTER_QUERY@ | ||
| @ADV_MAX_HITS@ | ||
| @ADV_WORD_SIZE@ | ||
| #if (str($adv_opts.identity_cutoff) and float(str($adv_opts.identity_cutoff)) > 0 ): | ||
| -perc_identity $adv_opts.identity_cutoff | ||
| -perc_identity '${adv_opts.identity_cutoff}' |
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Don't need quotes here, identity_cutoff is a float.
| #if str($adv_opts.matrix_gapcosts.matrix): | ||
| -matrix $adv_opts.matrix_gapcosts.matrix | ||
| $adv_opts.matrix_gapcosts.gap_costs | ||
| -matrix '${adv_opts.matrix_gapcosts.matrix}' |
| -qcov_hsp_perc $adv_opts.qcov_hsp_perc | ||
| <token name="@ADV_QCOV_HSP_PERC@"><![CDATA[ | ||
| #if float(str($adv_opts.qcov_hsp_perc)) > 0: | ||
| -qcov_hsp_perc '${adv_opts.qcov_hsp_perc}' |
| ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string | ||
| ## Note -max_target_seqs used to simply override -num_descriptions and -num_alignments | ||
| ## but this was changed in BLAST+ 2.2.27 onwards to force their use (raised with NCBI) | ||
| #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): | ||
| #if str($output.out_format) in ["6", "ext", "cols", "5"]: | ||
| ## Most output formats use this, including tabular and XML: | ||
| -max_target_seqs $adv_opts.max_hits | ||
| -max_target_seqs '${adv_opts.max_hits}' |
| #else | ||
| ## Text and HTML output formats 0-4 currently need this instead: | ||
| -num_descriptions $adv_opts.max_hits -num_alignments $adv_opts.max_hits | ||
| #end if | ||
| #end if | ||
| #if str($adv_opts.max_hsps) | ||
| -max_hsps $adv_opts.max_hsps | ||
| -max_hsps '${adv_opts.max_hsps}' |
| #if str($adv_opts.comp_based_stats): | ||
| -comp_based_stats $adv_opts.comp_based_stats | ||
| -comp_based_stats '${adv_opts.comp_based_stats}' |
| #if str($adv_opts.gapopen): | ||
| -gapopen $adv_opts.gapopen | ||
| -gapopen '${adv_opts.gapopen}' |
| #if str($adv_opts.gapextend): | ||
| -gapextend $adv_opts.gapextend | ||
| -gapextend '${adv_opts.gapextend}' |
| #if str($adv_opts.matrix): | ||
| -matrix $adv_opts.matrix | ||
| -matrix '${adv_opts.matrix}' |
| @@ -46,8 +55,8 @@ $hash_index | |||
| #end if | |||
| ## -------------------------------------------------------------------- | |||
| ## Capture the stdout log information to the primary file (plain text): | |||
| > "$outfile" | |||
| </command> | |||
| > "$outfile" | |||
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Oh, good catch on the outfile quotes.
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@nsoranzo You flagged a lot of the quoting Anton added as unnecessary - does the IUC have any thing more explicit to say on this beyond:
https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html |
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Not really, it's probably more of a de facto standard. I guess using quotes only when needed makes the final command shorter/cleaner and may help to spot errors. |
Hat tip Nicola Soranzo during pull request review.
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Thanks @nekrut - merged during the GCCBOSC 2018 CollaborationFest |
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