de9b6a3656
Clean up Makefile. Patch configure so that we can enable 3rd party software support more easily, fix missing options. Prefer to link dynamically. Changes since 2.29: - Added tblastn-fast, blastp-fast, and blastx-fast tasks. These tasks make use of longer words as described by Shiryev et al. in http://www.ncbi.nlm.nih.gov/pubmed/17921491. - Added new output option (outfmt 12) with Seq-Align in JSON. - Added new command line option qcov_hsp_perc that removes alignments below the specified query coverage. - Added option line_length for the printing of alignment lengths (outfmt 0-4). - Added larger gap penalties for PAM30 and PAM70 matrices. - psiblast now accepts 0 for num_iterations to indicate iterating until convergence. - rpsblast uses composition-based-statistics by default. Recover old behavior with "-comp_based_stats F -seg yes". - Improved blastn multithreading performance for many queries with small databases. - Changed cmdline option -sum_stats (formerly -sum_statistics) from flag to boolean. - Fixed spurious messages when parsing FASTA input. - Fixed makeprofiledb handling of PSSMs created from multiple sequence alignment. - Fixed makeblastdb handling of '-' at the end of FASTA input. - Fixed windowmasker segmentation fault when the incorrect window size is provided. - Fixed problem with lower-case masking and large sequences. - Fixed makeblastdb segmentation fault on duplicate seqids. - Allow specification of scoring matrices in lower case letters. - Fixed exit code when disk space is not available for the output file. - Fixed problem with using seqids list from -outfmt "6 sseqid" as input with --seqidlist. - Fixed bug with culling_limit that excludes top hit. - Fixed bug with max_target_seqs not working with psiblast.
12 lines
293 B
Makefile
12 lines
293 B
Makefile
# $NetBSD: buildlink3.mk,v 1.2 2014/10/08 12:44:35 fhajny Exp $
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BUILDLINK_TREE+= blast
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.if !defined(BLAST_BUILDLINK3_MK)
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BLAST_BUILDLINK3_MK:=
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BUILDLINK_API_DEPENDS.blast+= blast>=2.2.29
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BUILDLINK_PKGSRCDIR.blast?= ../../wip/ncbi-blast
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.endif # BLAST_BUILDLINK3_MK
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BUILDLINK_TREE+= -blast
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