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* Merge remote-tracking branch 'upstream/master'Koop Mast2019-09-2532-67/+347
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| * biology/py-multiqc: Aggregate bioinformatics analysis reportsjwb2019-09-246-0/+118
| * devel/openmp: update to 9.0.0jbeich2019-09-223-3/+3
| * biology/p5-TrimGalore: Upgrade to 0.6.4jwb2019-09-212-5/+5
| * biology/fastqc: Upgrade to 0.11.8jwb2019-09-213-14/+12
| * biology/diamond: Update to version 0.9.26jrm2019-09-192-4/+4
| * Fix some misspelled or duplicated LICENSE_*tobik2019-09-181-1/+1
| * biology/haplohseq: Identify regions of allelic imbalancejwb2019-09-168-0/+185
| * Deprecate a few portsantoine2019-09-162-0/+4
| * Drop C++11 workaround for GCC < 6 after r449590jbeich2019-09-152-36/+1
| * biology/trimmomatic: Upgrade to 0.39jwb2019-09-144-4/+14
* | Merge remote-tracking branch 'upstream/master'Koop Mast2019-09-1412-79/+84
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| * biology/bedtools: Upgrade to 2.29.0jwb2019-09-135-49/+64
| * biology/py-cutadapt: Upgrade to 2.5jwb2019-09-132-5/+6
| * biology/phyml: update to 3.3.20190909fernape2019-09-112-6/+6
| * Update to 1.007006 (1.7.6)sunpoet2019-09-083-19/+8
* | Merge remote-tracking branch 'upstream/master'Koop Mast2019-09-0710-22/+190
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| * Fix after gets(3) retirement using gets_s(3).cy2019-09-021-1/+1
| * Add a patch to remove use of gets(3)lwhsu2019-09-022-0/+169
| * biology/py-pysam: Update 0.15.2 -> 0.15.3yuri2019-08-312-4/+4
| * biology/ngs-sdk: Update 2.9.6 -> 2.10.0yuri2019-08-314-13/+13
| * biology/iqtree: Update to version 1.6.12jrm2019-08-272-5/+4
* | Merge remote-tracking branch 'upstream/master'Koop Mast2019-08-2413-41/+35
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| * biology/gperiodic: fix NLS and other rough edgespi2019-08-232-30/+22
| * devel/boost-*: update to 1.71.0jbeich2019-08-199-7/+9
| * biology/checkm: Update 1.0.17 -> 1.0.18yuri2019-08-192-4/+4
* | Merge remote-tracking branch 'upstream/master'Koop Mast2019-08-1529-201/+190
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| * Convert to UCL & cleanup pkg-message (categories a-c)mat2019-08-1413-32/+78
| * biology/bolt-lmm: Upgrade to 2.3.4jwb2019-08-137-120/+63
| * biology/checkm: Update 1.0.16 -> 1.0.17yuri2019-08-122-4/+4
| * biology/gperiodic: upgrade 2.0.10 -> 3.0.3pi2019-08-123-23/+39
| * Update to 1.007005 (1.7.5)sunpoet2019-08-123-20/+5
| * Update WWWsunpoet2019-08-111-1/+1
| * biology/checkm: Update 1.0.13 -> 1.0.16yuri2019-08-092-5/+4
* | Merge remote-tracking branch 'upstream/master'Koop Mast2019-08-0760-38/+160
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| * biology/hhsuite: fix build on powerpc64pkubaj2019-08-051-2/+7
| * PR: 239613jwb2019-08-056-1/+94
| * biology/diamond: Update to version 0.9.25jrm2019-08-052-4/+4
| * Mark BROKEN: unfetchableantoine2019-08-043-0/+6
| * Bump PORTREVISION for ports depending on the canonical version of GCCgerald2019-07-2750-32/+50
* | Merge remote-tracking branch 'upstream/master'Koop Mast2019-07-2713-16/+107
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| * biology/gatk: Update 4.0.11.0 -> 4.1.2.0-43yuri2019-07-272-12/+31
| * - Update WWWamdmi32019-07-251-1/+1
| * Prepare for devel/gradle4 and java/openjfx8-devel updatestobik2019-07-231-2/+2
| * biology/treekin: fix build on GCC architecturespkubaj2019-07-191-1/+2
| * ncbi-blast+: Unbreak build with gcc8 following gcc9 patchjwb2019-07-132-7/+9
| * New port: biology/libbigwig: C library for handling bigWig files (containing ...yuri2019-07-125-0/+54
| * ncbi-blast+: Fix build with gcc9jwb2019-07-111-0/+14
| * Update security/nettle to 3.5.1sunpoet2019-07-102-1/+2
| * - Update WWWamdmi32019-07-081-1/+1