{bio}[foss/2016b] MapSplice 2.2.1#5566
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| * fix build error with gcc >= 4.9: redeclaration of ... may not have default arguments | |||
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| sanity_check_paths = { | ||
| 'files': ['%(namelower)s.py'], | ||
| 'dirs': ['bin'], |
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@SethosII Since binaries are being built, I think it makes sense to specifically check for a couple of them (the main ones, if it's easy to tell which ones those are), rather than just checking for a non-empty bin directory.
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@boegel The bin directory contains a lot of binaries and I don't really know the main ones, but probably bowtie and samtools? Here is the list of binaries:
AddFusionStrandConsistent
alignment_handler
alignment_handler_multi
bowtie
bowtie-build
bowtie-inspect
bsb4
check_index_consistency
check_reads_format
cluster
collectstats
comp_fusiondb_offset
Convert2FusionAlignment
DNA2StdRegion
filter_1hits
FilterFusionAlignmentsByFilteredFusions
FilterFusionByNormalPaired
filterjuncbyROCarguNonCanonical
filteroriginalfusion
filterremappedfusion
find_mate_sam_fq
fusionsam2junc_filteranchor_newfmt
generate_combined_sequence
generate_fusiongene_convert_coordinate_trim
generate_fusiongene_convert_coordinate_trim_dRanger
gtf2genetab
junc2bed
junc_db
junc_db_fusion
load_fusion_chrom_seq_std
mapsplice_multi_thread
matchfusion2normal
MPSSam2fq
newsam2junc
parseCluster
read_chromo_size
reads2unmappedsam
recover_fusion_alignments_order
RemovePairNo
sam2fq
samtools
search_fusion_gene
search_unmapped_reads
SeparateNormalFromFusionJunc
sepdRangerfusion
sepMPSfusion
SepSam
SepSamUnmapped
SetUnmappedBitFlag
swap_dRanger_and_MPS_matched
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In that case, let's leave it as it...
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| patches = [ | ||
| '%(name)s-%(version)s_fix-build-gcc.patch', | ||
| ] |
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style nitpicking: collapse this to a single line, drop empty line before & after
sources = ['%(name)s-v%(version)s.zip']
patches = ['%(name)s-%(version)s_fix-build-gcc.patch']
checksums = [
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Test report by @boegel |
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Test report by @boegel |
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@boegel I updated the checksum. |
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Test report by @boegel |
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Test report by @boegel |
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Going in, thanks @SethosII! |
This adds MapSplice.
The patch is needed because since GCC version 4.9 default arguments on the definition are not allowed and have to be moved to the declaration. I also submitted the patch to the developers.