jwb (jwb@freebsd.org)
HPC Systems Programmer

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User Details

User Since
Nov 27 2017, 4:37 PM (21 w, 1 d)

Systems manager and facilitator for Research Computing at the University of Wisconsin -- Milwaukee

Recent Activity

Yesterday

jwb committed rP468214: biology/unanimity: Pacific Biosciences consensus library and applications.
biology/unanimity: Pacific Biosciences consensus library and applications
Tue, Apr 24, 2:17 PM
jwb closed D15172: biology/unanimity: Pacific Biosciences consensus library and applications.
Tue, Apr 24, 2:16 PM
jwb added a comment to D15172: biology/unanimity: Pacific Biosciences consensus library and applications.

Yep, 'been using this for years, at least in my wip ports. Very handy for persnickety genomics ports.

Tue, Apr 24, 4:35 AM

Mon, Apr 23

jwb created D15172: biology/unanimity: Pacific Biosciences consensus library and applications.
Mon, Apr 23, 5:19 PM
jwb committed rP468101: biology/pbcopper: Core C++ library for Pacific Biosciences tools.
biology/pbcopper: Core C++ library for Pacific Biosciences tools
Mon, Apr 23, 4:24 PM
jwb closed D15171: biology/pbcopper: Core C++ library for Pacific Biosciences tools.
Mon, Apr 23, 4:24 PM
jwb added a comment to D15154: biology/pbbam: PacBio BAM C++ library, with SWIG bindings.

No worries, I managed to find something else to do while I waited. ;-)

Mon, Apr 23, 4:18 PM
jwb created D15171: biology/pbcopper: Core C++ library for Pacific Biosciences tools.
Mon, Apr 23, 4:17 PM
jwb committed rP468100: biology/pbbam: PacBio BAM C++ library, with SWIG bindings.
biology/pbbam: PacBio BAM C++ library, with SWIG bindings
Mon, Apr 23, 4:08 PM
jwb closed D15154: biology/pbbam: PacBio BAM C++ library, with SWIG bindings.
Mon, Apr 23, 4:08 PM

Sat, Apr 21

jwb created D15154: biology/pbbam: PacBio BAM C++ library, with SWIG bindings.
Sat, Apr 21, 9:08 PM
jwb committed rP467901: biology/pbseqan: Pacific Biosciences patched and stripped down SeqAn.
biology/pbseqan: Pacific Biosciences patched and stripped down SeqAn
Sat, Apr 21, 5:21 PM
jwb closed D15152: biology/pbseqan: Pacific Biosciences patched and stripped down SeqAn.
Sat, Apr 21, 5:21 PM
jwb updated the diff for D15152: biology/pbseqan: Pacific Biosciences patched and stripped down SeqAn.

Good catch. I deliberately left it out because it's a compiled language,
but forgot that it's only installing headers.

Sat, Apr 21, 5:08 PM
jwb created D15152: biology/pbseqan: Pacific Biosciences patched and stripped down SeqAn.
Sat, Apr 21, 4:20 PM

Fri, Apr 20

jwb closed D15139: biology/ddocent: Bash pipeline for RAD sequencing.
Fri, Apr 20, 1:34 AM
jwb committed rP467808: biology/ddocent: Bash pipeline for RAD sequencing.
biology/ddocent: Bash pipeline for RAD sequencing
Fri, Apr 20, 1:34 AM
jwb added a comment to D15139: biology/ddocent: Bash pipeline for RAD sequencing.

Don't stop making suggestions until I stop making mistakes. ;-)

Fri, Apr 20, 1:30 AM
jwb updated the diff for D15139: biology/ddocent: Bash pipeline for RAD sequencing.

I think biology/Makefile should match the directory name, not PKGBASE.

Fri, Apr 20, 1:16 AM
jwb created D15139: biology/ddocent: Bash pipeline for RAD sequencing.
Fri, Apr 20, 12:32 AM
jwb committed rP467806: biology/freebayes: Bayesian haplotype-based polymorphism discovery and….
biology/freebayes: Bayesian haplotype-based polymorphism discovery and…
Fri, Apr 20, 12:07 AM
jwb closed D15116: Bayesian haplotype-based polymorphism discovery and genotyping.
Fri, Apr 20, 12:07 AM
jwb added a comment to D15116: Bayesian haplotype-based polymorphism discovery and genotyping.

Well that's interesting... A couple days ago SeqLib was behaving like vcflib, ending up empty except for the subdirectories. I only noticed it after the vcflib patch failed and I realized that these are the two submodules with submodules. I don't think I trust this new development, so I'll leave the hack in until we get to the bottom of this.

Fri, Apr 20, 12:03 AM

Thu, Apr 19

jwb added a comment to D15116: Bayesian haplotype-based polymorphism discovery and genotyping.

What were you saying about the vcflib contents? Here's what I'm seeing:

Thu, Apr 19, 11:03 PM
jwb committed rP467783: biology/bedtools: Upgrade to 2.27.1.
biology/bedtools: Upgrade to 2.27.1
Thu, Apr 19, 4:45 PM
jwb closed D15137: biology/bedtools: Upgrade to 2.27.1.
Thu, Apr 19, 4:45 PM
jwb updated the diff for D15137: biology/bedtools: Upgrade to 2.27.1.

I don't know why it was added originally, but I've built the new version
at least a dozen times without it and run it through poudriere testport
twice on all platforms, so I'm pretty confident.

Thu, Apr 19, 4:22 PM
jwb created D15137: biology/bedtools: Upgrade to 2.27.1.
Thu, Apr 19, 3:51 PM

Wed, Apr 18

jwb added a comment to D15116: Bayesian haplotype-based polymorphism discovery and genotyping.

Yeah, I get the same problem with SeqLib and vcflib, as both of them have submodules. If I list them directly in GH_TUPLE, they get blanked when their submodules are moved into place. I didn't notice it at first with SeqLib, because there are no patches in that directory. patch-vcflib_Makefile failed when I added ekg:fastahack:c68cebb:fastahack/vcflib/fastahack, which is what tipped me off to the problem.

Wed, Apr 18, 6:04 AM

Tue, Apr 17

jwb updated the diff for D15116: Bayesian haplotype-based polymorphism discovery and genotyping.

Yeah, I didn't bother testing this one as I'm hoping for some discussion
before I commit. Should have done so anyway. I'm going to script the
import process to remove the wip category, run port-check, and open
category/Makefile so I won't miss anything in the future.

Tue, Apr 17, 6:05 PM
jwb created D15116: Bayesian haplotype-based polymorphism discovery and genotyping.
Tue, Apr 17, 3:05 PM
jwb committed rP467553: biology/vcflib: C++ library and CLI tools for parsing and manipulating VCF files.
biology/vcflib: C++ library and CLI tools for parsing and manipulating VCF files
Tue, Apr 17, 3:11 AM
jwb closed D15109: C++ library and CLI tools for parsing and manipulating VCF files.
Tue, Apr 17, 3:11 AM

Mon, Apr 16

jwb created D15109: C++ library and CLI tools for parsing and manipulating VCF files.
Mon, Apr 16, 10:39 PM
jwb committed rP467529: math/intervaltree: Remove invalid category.
math/intervaltree: Remove invalid category
Mon, Apr 16, 7:18 PM
jwb committed rP467527: math/intervaltree: Minimal C++ interval tree implementation.
math/intervaltree: Minimal C++ interval tree implementation
Mon, Apr 16, 6:56 PM
jwb closed D15105: math/intervaltree: Minimal C++ interval tree implementation.
Mon, Apr 16, 6:56 PM
jwb created D15105: math/intervaltree: Minimal C++ interval tree implementation.
Mon, Apr 16, 6:43 PM
jwb committed rP467502: math/multichoose: Generate multiset combinations (n multichoose k).
math/multichoose: Generate multiset combinations (n multichoose k)
Mon, Apr 16, 6:32 PM
jwb closed D15104: math/multichoose: Generate multiset combinations (n multichoose k).
Mon, Apr 16, 6:32 PM
jwb created D15104: math/multichoose: Generate multiset combinations (n multichoose k).
Mon, Apr 16, 6:21 PM
jwb committed rP467501: fsom: Tiny C library for managing SOM (Self-Organizing Maps) neural networks.
fsom: Tiny C library for managing SOM (Self-Organizing Maps) neural networks
Mon, Apr 16, 6:15 PM
jwb closed D15103: fsom: Tiny C library for managing SOM (Self-Organizing Maps) neural networks.
Mon, Apr 16, 6:15 PM
jwb created D15103: fsom: Tiny C library for managing SOM (Self-Organizing Maps) neural networks.
Mon, Apr 16, 6:07 PM
jwb committed rP467487: sysutils/filevercmp: Compare version strings as in sort --version-sort.
sysutils/filevercmp: Compare version strings as in sort --version-sort
Mon, Apr 16, 4:22 PM
jwb closed D15098: sysutils/filevercmp: Compare version strings as in sort --version-sort.
Mon, Apr 16, 4:21 PM
jwb added a comment to D15098: sysutils/filevercmp: Compare version strings as in sort --version-sort.

I'm not sure, actually. It's a dependency for vcflib and possibly other github/ekg tools. I'd rather not try to hack dependent ports to use a pkg command as I'd have to verify that it behaves exactly the same as this tool every time either one is updated.

Mon, Apr 16, 3:51 PM
jwb created D15098: sysutils/filevercmp: Compare version strings as in sort --version-sort.
Mon, Apr 16, 2:59 PM
jwb committed rP467485: biology/fastahack: Utility for indexing and sequence extraction from FASTA files.
biology/fastahack: Utility for indexing and sequence extraction from FASTA files
Mon, Apr 16, 2:50 PM
jwb closed D15080: biology/fastahack: Utility for indexing and sequence extraction from FASTA files.
Mon, Apr 16, 2:50 PM

Sun, Apr 15

jwb created D15080: biology/fastahack: Utility for indexing and sequence extraction from FASTA files.
Sun, Apr 15, 11:29 PM
jwb closed D15072: biology/smithwaterman: Smith-waterman-gotoh alignment algorithm.
Sun, Apr 15, 5:46 PM
jwb committed rP467402: biology/smithwaterman: Smith-waterman-gotoh alignment algorithm.
biology/smithwaterman: Smith-waterman-gotoh alignment algorithm
Sun, Apr 15, 5:46 PM
jwb updated the diff for D15072: biology/smithwaterman: Smith-waterman-gotoh alignment algorithm.

I was actually following Example 5.13 on the DISTVERSION.

Sun, Apr 15, 11:43 AM
jwb created D15072: biology/smithwaterman: Smith-waterman-gotoh alignment algorithm.
Sun, Apr 15, 5:25 AM

Sat, Apr 14

jwb committed rP467343: biology/tabixpp: C++ wrapper to tabix indexer.
biology/tabixpp: C++ wrapper to tabix indexer
Sat, Apr 14, 11:52 PM
jwb closed D14977: biology/tabixpp: C++ wrapper to tabix indexer.
Sat, Apr 14, 11:52 PM

Sat, Apr 7

jwb updated the diff for D14977: biology/tabixpp: C++ wrapper to tabix indexer.

Human because he expected me to notice the missing lib/? ;-)

Sat, Apr 7, 10:26 PM

Fri, Apr 6

jwb updated the diff for D14977: biology/tabixpp: C++ wrapper to tabix indexer.

Interesting. I would not have thought to use anything outside WRKSRC in the
build.

Fri, Apr 6, 1:48 PM

Thu, Apr 5

jwb updated the diff for D14977: biology/tabixpp: C++ wrapper to tabix indexer.

localbase:ldflags is what I was looking for...

Thu, Apr 5, 7:32 PM
jwb created D14977: biology/tabixpp: C++ wrapper to tabix indexer.
Thu, Apr 5, 4:13 PM

Wed, Apr 4

jwb committed rP466449: biology/pear-merger: Memory-efficient and accurate paired-end read merger.
biology/pear-merger: Memory-efficient and accurate paired-end read merger
Wed, Apr 4, 5:21 PM
jwb closed D14959: biology/pear-merger: Memory-efficient and highly accurate paired-end read merger.
Wed, Apr 4, 5:21 PM
jwb created D14959: biology/pear-merger: Memory-efficient and highly accurate paired-end read merger.
Wed, Apr 4, 4:05 AM

Tue, Apr 3

jwb committed rP466379: biology/seqtk: Tool for processing sequences in FASTA/FASTQ format.
biology/seqtk: Tool for processing sequences in FASTA/FASTQ format
Tue, Apr 3, 8:57 PM
jwb closed D14954: Tool for processing sequences in FASTA/FASTQ format.
Tue, Apr 3, 8:57 PM
jwb created D14954: Tool for processing sequences in FASTA/FASTQ format.
Tue, Apr 3, 6:44 PM
jwb committed rP466367: biology/trimadap: Trim adapter sequences from Illumina data.
biology/trimadap: Trim adapter sequences from Illumina data
Tue, Apr 3, 6:24 PM
jwb closed D14935: biology/trimadap: Trim adapter sequences from Illumina data.
Tue, Apr 3, 6:24 PM
jwb added a comment to D14935: biology/trimadap: Trim adapter sequences from Illumina data.

Agreed. Now that I'm aware of all the USE_GITHUB support for cases like this, I am definitely inclined to utilize it.

Tue, Apr 3, 6:23 PM
jwb updated the diff for D14935: biology/trimadap: Trim adapter sequences from Illumina data.

I see, I was only looking at the Naming section and didn't realize there was
more about this under USE_GITHUB. This is very nice...

Tue, Apr 3, 4:38 PM
jwb added a comment to D14935: biology/trimadap: Trim adapter sequences from Illumina data.

Maybe you're looking at the p20170211 as a pre-release level? It's actually a post-release patch level. 0.1.p20170211 would be a pre-release, 0.1p20170211 is a patch level. Rather confusing, I think, but at least it's documented. We had a discussion about this a couple months ago and concluded that using PORTVERSION is the only way to specify a patch level.

Tue, Apr 3, 3:48 PM
jwb updated the diff for D14935: biology/trimadap: Trim adapter sequences from Illumina data.

I like it... Thanks.

Tue, Apr 3, 3:12 PM

Mon, Apr 2

jwb created D14935: biology/trimadap: Trim adapter sequences from Illumina data.
Mon, Apr 2, 6:19 PM
jwb committed rP466235: biology/rainbow: Efficient clustering and assembling of short reads.
biology/rainbow: Efficient clustering and assembling of short reads
Mon, Apr 2, 4:51 PM
jwb closed D14924: biology/rainbow: Efficient clustering and assembling of short reads.
Mon, Apr 2, 4:51 PM
jwb updated the diff for D14924: biology/rainbow: Efficient clustering and assembling of short reads.

wip: Just seeing if you were paying attention. ;-)

Mon, Apr 2, 2:08 AM

Sun, Apr 1

jwb created D14924: biology/rainbow: Efficient clustering and assembling of short reads.
Sun, Apr 1, 4:08 PM

Sat, Mar 31

jwb committed rP466048: biology/stacks: Software pipeline for building loci from short-read sequences.
biology/stacks: Software pipeline for building loci from short-read sequences
Sat, Mar 31, 1:16 PM
jwb closed D14885: biology/stacks: Software pipeline for building loci from short-read sequences.
Sat, Mar 31, 1:16 PM
jwb added a comment to D14885: biology/stacks: Software pipeline for building loci from short-read sequences.

Yes, I was focused this time around. I've always been good during exams. ;-)

Sat, Mar 31, 1:14 PM
jwb added a comment to D14909: sysutils/htcondor: Unbreak and upgrade to 8.4.12.

I think I copy/pasted that line late in the game, after checking for += lint. Note that I fixed LIB_DEPENDS and CMAKE_ARGS, but then missed this one. I fixed it in the WIP port so it will be corrected in the next commit. Thanks!

Sat, Mar 31, 12:59 PM
jwb added a comment to D14885: biology/stacks: Software pipeline for building loci from short-read sequences.

Are you referring to LDFLAGS+=? If so, I think that should be left as-is.

Sat, Mar 31, 12:51 AM
jwb committed rP466017: sysutils/htcondor: Unbreak and upgrade to 8.4.12.
sysutils/htcondor: Unbreak and upgrade to 8.4.12
Sat, Mar 31, 12:37 AM
jwb closed D14909: sysutils/htcondor: Unbreak and upgrade to 8.4.12.
Sat, Mar 31, 12:37 AM
jwb added a comment to D14885: biology/stacks: Software pipeline for building loci from short-read sequences.

Regarding GNU_CONFIGURE: Yeah, I've always read this as "USES_GNU_CONFIGURE", so it seems logical to keep it in the USES section. Thanks...

Sat, Mar 31, 12:32 AM
jwb updated the diff for D14885: biology/stacks: Software pipeline for building loci from short-read sequences.

Here's the best I can come up with short of setting up a web server and
testing, which I don't have time for. I'm not sure we have anyone here who
would know how to use it anyway. At least this points potential users in
the right direction.

Sat, Mar 31, 12:29 AM

Fri, Mar 30

jwb added a comment to D14909: sysutils/htcondor: Unbreak and upgrade to 8.4.12.

I think that's worth exploring, but I'd rather wait until the next commit rather than potentially introduce a regression under time pressure.

Fri, Mar 30, 11:52 PM
jwb added a comment to D14885: biology/stacks: Software pipeline for building loci from short-read sequences.

Good idea. We don't use stacks directly here, only as a dependency for ddocent, which people run on our clusters. I'll take a look at how it might be used on a desktop machine and make some adjustments along the line you suggested.

Fri, Mar 30, 3:50 PM
jwb created D14909: sysutils/htcondor: Unbreak and upgrade to 8.4.12.
Fri, Mar 30, 3:44 PM

Thu, Mar 29

jwb added a comment to D14892: biology/libgtextutils: Unbreak for FreeBSD 12.

Updated my checklist so this won't happen again.

Thu, Mar 29, 3:49 PM
jwb added a comment to D14892: biology/libgtextutils: Unbreak for FreeBSD 12.

Crap, sorry. I didn't scroll down to see your comment. I'm just overwhelmed with juggling too many things here...

Thu, Mar 29, 3:45 PM
jwb closed D14892: biology/libgtextutils: Unbreak for FreeBSD 12.
Thu, Mar 29, 3:41 PM
jwb committed rP465904: biology/libgtextutils: Unbreak for FreeBSD 12.
biology/libgtextutils: Unbreak for FreeBSD 12
Thu, Mar 29, 3:41 PM
jwb created D14892: biology/libgtextutils: Unbreak for FreeBSD 12.
Thu, Mar 29, 1:46 PM

Wed, Mar 28

jwb created D14885: biology/stacks: Software pipeline for building loci from short-read sequences.
Wed, Mar 28, 5:25 PM
jwb added a comment to D14877: biology/bamtools: API and toolkit for handling BAM files.

I'll leave it alone for now rather than add noise to the commit log.

Wed, Mar 28, 3:03 PM
jwb added a comment to D14877: biology/bamtools: API and toolkit for handling BAM files.

Do you consider this worth another commit, or should it wait until the next upgrade?

Wed, Mar 28, 2:19 PM
jwb added a comment to D14877: biology/bamtools: API and toolkit for handling BAM files.

Yes, I did overlook your comment.

Wed, Mar 28, 2:13 PM
jwb committed rP465808: biology/bamtools: API and toolkit for handling BAM files.
biology/bamtools: API and toolkit for handling BAM files
Wed, Mar 28, 1:26 PM