debian/changelog

+pbbarcode (0.8.0-6) UNRELEASED; urgency=medium
+
+  * Use 2to3 to port to Python3
+    Closes: #937253
+  * debhelper-compat 12
+  * Standards-Version: 4.4.1
+  * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
+  * Set upstream metadata fields: Repository, Repository-Browse.
+  TODO: #938009 (python-pbcore)
+
+ -- Andreas Tille <tille@debian.org>  Sat, 30 Nov 2019 17:59:51 +0100
+
 pbbarcode (0.8.0-5) unstable; urgency=medium
 
   * Team upload.

debian/compat

-11

debian/control

@@ -2,18 +2,18 @@ Source: pbbarcode
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                dh-python,
-               python-setuptools,
+               python3-setuptools,
                python3-docutils,
-               python-all-dev,
-               python-pbcore,
-               python-numpy,
-               python-h5py,
+               python3-all-dev,
+               python3-pbcore,
+               python3-numpy,
+               python3-h5py,
 # Test-Depends:
-               python-nose,
+               python3-nose,
                pbh5tools
-Standards-Version: 4.2.1
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/pbbarcode
 Vcs-Git: https://salsa.debian.org/med-team/pbbarcode.git
 Homepage: https://github.com/PacificBiosciences/pbbarcode
@@ -22,8 +22,8 @@ Package: pbbarcode
 Architecture: any
 Depends: ${misc:Depends},
          ${shlibs:Depends},
-         ${python:Depends},
-         python-pkg-resources
+         ${python3:Depends},
+         python3-pkg-resources
 Suggests: pbdagcon
 Description: annotate PacBio sequencing reads with barcode information
  The pbbarcode package provides tools for annotating PacBio sequencing reads

debian/patches/2to3.patch

+Description: Use 2to3 to port to Python3
+Bug-Debian: https://bugs.debian.org/937253
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Sat, 30 Nov 2019 17:59:51 +0100
+
+--- a/Makefile
++++ b/Makefile
+@@ -5,17 +5,17 @@ SHELL = /bin/bash -e
+ all: build install
+ 
+ build:
+-	python setup.py build --executable="/usr/bin/env python"
++	python3 setup.py build --executable="/usr/bin/python3"
+ 
+ bdist:
+-	python setup.py build --executable="/usr/bin/env python"
+-	python setup.py bdist --formats=egg
++	python3 setup.py build --executable="/usr/bin/python3"
++	python3 setup.py bdist --formats=egg
+ 
+ install:
+-	python setup.py install
++	python3 setup.py install
+ 
+ develop:
+-	python setup.py develop
++	python3 setup.py develop
+ 
+ test:
+ 	find tests -name "*.py" | xargs nosetests
+--- a/doc/conf.py
++++ b/doc/conf.py
+@@ -40,8 +40,8 @@ source_suffix = '.rst'
+ master_doc = 'index'
+ 
+ # General information about the project.
+-project = u'pbbarcode'
+-copyright = u'2012, PacBio'
++project = 'pbbarcode'
++copyright = '2012, PacBio'
+ 
+ # The version info for the project you're documenting, acts as replacement for
+ # |version| and |release|, also used in various other places throughout the
+@@ -183,8 +183,8 @@ latex_elements = {
+ # Grouping the document tree into LaTeX files. List of tuples
+ # (source start file, target name, title, author, documentclass [howto/manual]).
+ latex_documents = [
+-  ('index', 'pbbarcode.tex', u'pbbarcode Documentation',
+-   u'PacBio', 'manual'),
++  ('index', 'pbbarcode.tex', 'pbbarcode Documentation',
++   'PacBio', 'manual'),
+ ]
+ 
+ # The name of an image file (relative to this directory) to place at the top of
+@@ -213,8 +213,8 @@ latex_documents = [
+ # One entry per manual page. List of tuples
+ # (source start file, name, description, authors, manual section).
+ man_pages = [
+-    ('index', 'pbbarcode', u'pbbarcode Documentation',
+-     [u'PacBio'], 1)
++    ('index', 'pbbarcode', 'pbbarcode Documentation',
++     ['PacBio'], 1)
+ ]
+ 
+ # If true, show URL addresses after external links.
+@@ -227,8 +227,8 @@ man_pages = [
+ # (source start file, target name, title, author,
+ #  dir menu entry, description, category)
+ texinfo_documents = [
+-  ('index', 'pbbarcode', u'pbbarcode Documentation',
+-   u'PacBio', 'pbbarcode', 'One line description of project.',
++  ('index', 'pbbarcode', 'pbbarcode Documentation',
++   'PacBio', 'pbbarcode', 'One line description of project.',
+    'Miscellaneous'),
+ ]
+ 
+--- a/src/python/pbbarcode/BarcodeLabeler.py
++++ b/src/python/pbbarcode/BarcodeLabeler.py
+@@ -35,8 +35,9 @@ import numpy as n
+ 
+ from pbcore.io.BarcodeH5Reader import LabeledZmw, \
+     BARCODE_DELIMITER
++from functools import reduce
+ 
+-__RC_MAP__ = dict(zip('ACGTacgt-N','TGCAtgca-N'))
++__RC_MAP__ = dict(list(zip('ACGTacgt-N','TGCAtgca-N')))
+ 
+ class BarcodeScorer(object):
+     def __init__(self, basH5, barcodeFasta,  
+@@ -53,8 +54,7 @@ class BarcodeScorer(object):
+         self.basH5 = basH5
+         self.barcodeFasta = list(barcodeFasta)
+         self.aligner = Aligner.SWaligner()
+-        self.barcodeLength = n.unique(map(lambda x : len(x.sequence), 
+-                                          self.barcodeFasta))
++        self.barcodeLength = n.unique([len(x.sequence) for x in self.barcodeFasta])
+         if len(self.barcodeLength) > 1:
+             raise Exception("Currently, all barcodes must be the same length.")
+         else:
+@@ -96,7 +96,7 @@ class BarcodeScorer(object):
+         if self.scoreMode == 'paired':
+             return n.array([self.makeBCLabel(self.barcodeFasta[i].name,
+                                              self.barcodeFasta[i+1].name) for i
+-                            in xrange(0, len(self.barcodeSeqs), 2)])
++                            in range(0, len(self.barcodeSeqs), 2)])
+         else:
+             return n.array([self.makeBCLabel(x.name, x.name) for x in self.barcodeFasta])
+ 
+@@ -193,7 +193,7 @@ class BarcodeScorer(object):
+         def choosePaired(o):
+             if o[1] == 1:
+                 s = n.array([max(o[2][i], o[2][i + 1]) for i in \
+-                                 xrange(0, len(self.barcodeSeqs), 2)])
++                                 range(0, len(self.barcodeSeqs), 2)])
+                 p = n.argsort(-s)
+                 s = s[p]
+             else:
+@@ -202,9 +202,9 @@ class BarcodeScorer(object):
+                 # missed adapter will confuse this computation.
+                 scores  = o[3]
+                 results = n.zeros(len(self.barcodeSeqs)/2)
+-                for i in xrange(0, len(self.barcodeSeqs), 2):
++                for i in range(0, len(self.barcodeSeqs), 2):
+                     pths = [0,0]
+-                    for j in xrange(0, len(scores)):
++                    for j in range(0, len(scores)):
+                         pths[j % 2] += scores[j][i]
+                         pths[1 - j % 2] += scores[j][i + 1]
+                     results[i/2] = max(pths)
+--- a/src/python/pbbarcode/SWaligner.py
++++ b/src/python/pbbarcode/SWaligner.py
+@@ -65,7 +65,7 @@ class SWaligner(object):
+                                            self.dpMat, 
+                                            query,
+                                            targetSeqs)
+-            return numpy.array([scores[i] for i in xrange(0, len(scores))])
++            return numpy.array([scores[i] for i in range(0, len(scores))])
+         return scorer
+ 
+         
+--- a/src/python/pbbarcode/main.py
++++ b/src/python/pbbarcode/main.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ #################################################################################$$
+ # Copyright (c) 2011,2012, Pacific Biosciences of California, Inc.
+ #
+@@ -55,6 +55,7 @@ from pbbarcode.BarcodeLabeler import *
+ from pbbarcode._version import __version__
+ 
+ from pbh5tools.CmpH5Utils import copyAttributes
++from functools import reduce
+ 
+ # Paths to the Barcode Datasets in the cmp.h5 file.
+ BC_ALN_INFO_DS = "AlnInfo/Barcode"
+@@ -110,7 +111,7 @@ def makeBarcodeFofnFromBasFofn():
+ 
+     logging.debug("Using %d processes." % runner.args.nProcs)
+     if runner.args.nProcs <= 1:
+-        newFiles = map(mpWrapper, inFiles)
++        newFiles = list(map(mpWrapper, inFiles))
+     else:
+         pool = Pool(runner.args.nProcs)
+         newFiles = pool.map(mpWrapper, inFiles)
+@@ -158,7 +159,7 @@ def labelAlignments():
+     # we use the first one to get the labels, if somehow they
+     # don't have all of the same stuff that will be an issue.
+     bcLabels = n.concatenate((bcFofn.barcodeLabels, n.array([BARCODE_DELIMITER]))) 
+-    H5.create_dataset(BC_INFO_ID, data = n.array(range(0, len(bcLabels))), 
++    H5.create_dataset(BC_INFO_ID, data = n.array(list(range(0, len(bcLabels)))), 
+                       dtype = 'int32')
+     H5.create_dataset(BC_INFO_NAME, data = bcLabels, dtype = h5.new_vlen(str))
+     if BC_ALN_INFO_DS in H5:
+@@ -180,17 +181,17 @@ def zipFofns(*inFofns):
+         return lines
+ 
+     sortedFofns = [readAndSort(inFofn) for inFofn in inFofns]
+-    l = map(len, sortedFofns)
++    l = list(map(len, sortedFofns))
+     if len(n.unique(l)) != 1:
+         raise Exception("Fofns don't match, unequal number of inputs.")
+     else:
+-        for i in xrange(0, n.unique(l)):
++        for i in range(0, n.unique(l)):
+             if len(n.unique([movieNameFromFile(sortedFofn[i]) for 
+                              sortedFofn in sortedFofns])) != 1:
+                 raise Exception("Fofn elements don't match, movies differ.")
+     
+     # need to un-arrayify these guys
+-    return zip(*map(list, sortedFofns))
++    return list(zip(*list(map(list, sortedFofns))))
+ 
+ def filterZmws(zmwsForBCs):
+     """Apply various filterings passed by the user. There are somewhat
+@@ -209,7 +210,7 @@ def filterZmws(zmwsForBCs):
+ 
+     def molLenGuess(zmw):
+         if zmw.baxH5.hasRawBasecalls:
+-            return max(map(len, zmw.subreads)) if zmw.subreads else 0
++            return max(list(map(len, zmw.subreads))) if zmw.subreads else 0
+         else:
+             return len(zmw.ccsRead) if zmw.ccsRead else 0
+ 
+@@ -237,7 +238,7 @@ def filterZmws(zmwsForBCs):
+         else:
+             return True
+ 
+-    return { k:filter(zmwFilterFx, v) for k,v in zmwsForBCs.items() }
++    return { k:list(filter(zmwFilterFx, v)) for k,v in list(zmwsForBCs.items()) }
+ 
+ def _warnOnce():
+     var = []
+@@ -276,18 +277,18 @@ def getFastqRecords(zmw, lZmw = None):
+ def getFastqs():
+     zmwsByBarcode = getZmwsForBarcodes()
+     logging.debug("Pre-filter: Average number of ZMWs per barcode: %d" % 
+-                  n.mean([len(zmwsByBarcode[k]) for k in zmwsByBarcode.keys()]))
++                  n.mean([len(zmwsByBarcode[k]) for k in list(zmwsByBarcode.keys())]))
+ 
+     zmwsByBarcode = filterZmws(zmwsByBarcode) 
+     logging.debug("Post-filter: Average number of ZMWs per barcode: %d" % 
+-                  n.mean([len(zmwsByBarcode[k]) for k in zmwsByBarcode.keys()]))
++                  n.mean([len(zmwsByBarcode[k]) for k in list(zmwsByBarcode.keys())]))
+     
+     def getReadData(zmws):
+         recs = [getFastqRecords(zmw,lZmw) for zmw,lZmw in zmws]
+-        recs = filter(lambda x : x, recs)
++        recs = [x for x in recs if x]
+         return [elt for sublst in recs for elt in sublst]
+ 
+-    return {k:getReadData(zmws) for k, zmws in zmwsByBarcode.iteritems()}
++    return {k:getReadData(zmws) for k, zmws in zmwsByBarcode.items()}
+ 
+ def emitFastqs():
+     outFiles = getFastqs()
+@@ -309,7 +310,7 @@ def emitFastqs():
+         record = FastqRecord
+     
+     l = 'a' if runner.args.fasta else 'q'
+-    for k in outFiles.keys():
++    for k in list(outFiles.keys()):
+         if outFiles[k]:
+             with writer("%s/%s.fast%s" % (runner.args.outDir, k, l)) as w:
+                 for e in outFiles[k]:
+@@ -328,7 +329,7 @@ def getUnlabeledZmws():
+         basH5 = BasH5Reader(basFile)
+         bcH5  = BarcodeH5Reader(barcodeFile)
+         sdiff = basH5.sequencingZmws[~n.in1d(basH5.sequencingZmws,  
+-                                             bcH5.labeledZmws.keys())]
++                                             list(bcH5.labeledZmws.keys()))]
+         for hn in sdiff:
+             unlabeledZmws.append(basH5[hn])
+ 
+@@ -351,7 +352,7 @@ def getZmwsForBarcodes(labels = None):
+             lZmws = bcH5.labeledZmwsFromBarcodeLabel(label)
+             for lZmw in lZmws:
+                 zmw = basH5[lZmw.holeNumber]
+-                if not label in zmwsForBCs.keys():
++                if not label in list(zmwsForBCs.keys()):
+                     zmwsForBCs[label] = []
+                 zmwsForBCs[label].append((zmw, lZmw))
+ 
+@@ -424,13 +425,13 @@ def subsampleReads(e):
+         k = int(len(e)*runner.args.subsample)
+     else:
+         k = len(e)
+-    i = n.array(random.sample(range(0, len(e)), k), dtype = int)
++    i = n.array(random.sample(list(range(0, len(e))), k), dtype = int)
+     logging.debug("subsampled down to: %d" % len(i))
+     return [e[j] for j in i]
+ 
+ def callConsensus():
+     def makeReadAndReads(zmwsForBC):
+-        ccsData = filter(lambda x:x, [zmw.ccsRead for _,_,zmw in zmwsForBC if zmw])
++        ccsData = [x for x in [zmw.ccsRead for _,_,zmw in zmwsForBC if zmw] if x]
+         srData  = reduce(lambda x,y : x+y, [zmw.subreads for zmw,_,_ in
+                                             zmwsForBC if zmw], [])
+         if not srData and not ccsData:
+@@ -438,7 +439,7 @@ def callConsensus():
+ 
+         def getSeedRead(reads, lq = 80, uq = 90, 
+                         sLambda = lambda x : -x.zmw.readScore):
+-            lens = map(len, reads)
++            lens = list(map(len, reads))
+             candidateRange = (n.percentile(lens, lq), 
+                               n.percentile(lens, uq))
+             pfReads = [read for read,l in zip(reads, lens) if 
+@@ -476,16 +477,16 @@ def callConsensus():
+         zmwsForBCs = getZmwsForBarcodes()
+     
+     # subsample
+-    zmwsForBCs = {k:subsampleReads(v) for k,v in zmwsForBCs.items()}
++    zmwsForBCs = {k:subsampleReads(v) for k,v in list(zmwsForBCs.items())}
+ 
+     logging.info("unfiltered average zmws per barcode: %g" % 
+-                 n.round(n.mean(map(len, zmwsForBCs.values()))))
++                 n.round(n.mean(list(map(len, list(zmwsForBCs.values()))))))
+ 
+     # filter ZMWs
+     zmwsForBCs = filterZmws(zmwsForBCs)
+     
+     logging.info("filtered average zmws per barcode: %g" % 
+-                 n.round(n.mean(map(len, zmwsForBCs.values()))))
++                 n.round(n.mean(list(map(len, list(zmwsForBCs.values()))))))
+ 
+     # now choose the best subread to seed the assembly
+     if runner.args.ccsFofn:
+@@ -496,7 +497,7 @@ def callConsensus():
+                       open(runner.args.ccsFofn).read().splitlines()}
+         
+         # fill in the CCS spot.
+-        for k,v in zmwsForBCs.items():
++        for k,v in list(zmwsForBCs.items()):
+             l = []
+             for zmw,lZmw in v:
+                 r = ccsReaders[movieNameFromFile(zmw.baxH5.file.filename)]
+@@ -505,17 +506,17 @@ def callConsensus():
+     else:
+         # add none to the CCS spot.
+         zmwsForBCs = {k:[(zmw,lZmw,None) for zmw,lZmw in v] 
+-                      for k,v in zmwsForBCs.iteritems()}
++                      for k,v in zmwsForBCs.items()}
+ 
+-    readAndReads = { k:makeReadAndReads(v) for k,v in zmwsForBCs.items() }
++    readAndReads = { k:makeReadAndReads(v) for k,v in list(zmwsForBCs.items()) }
+ 
+     # remove barcodes that don't have a seed read and a set of useable reads.
+-    readAndReads = { k:v for k,v in readAndReads.items() if v[0] and v[1] }
++    readAndReads = { k:v for k,v in list(readAndReads.items()) if v[0] and v[1] }
+    
+     # generate FASTA files
+     outDir = runner.args.outDir
+ 
+-    for barcode, reads in readAndReads.items():
++    for barcode, reads in list(readAndReads.items()):
+         bcdir = '/'.join((outDir, barcode))
+         if not os.path.exists(bcdir):
+             os.makedirs(bcdir)
+@@ -537,8 +538,7 @@ def callConsensus():
+         for inFof, in zipFofns(runner.args.inputFofn):
+             bh5 = BaxH5Reader(inFof)
+             reg = bh5.file['/PulseData/Regions']
+-            inMovie = filter(lambda z : z.baxH5.movieName == bh5.movieName, 
+-                             subreads)
++            inMovie = [z for z in subreads if z.baxH5.movieName == bh5.movieName]
+             holes = n.in1d(reg[:,0], n.array([a.holeNumber for a in inMovie]))
+             if any(holes): 
+                 nreg = reg[holes,:]
+@@ -558,12 +558,12 @@ def callConsensus():
+         ofile.close()
+     
+     ## call gcon
+-    outDirs  = [ (outDir, k) for k in readAndReads.keys() ]
++    outDirs  = [ (outDir, k) for k in list(readAndReads.keys()) ]
+     if runner.args.nProcs == 1:
+-        outFasta = filter(lambda z: z, map(gconFunc, outDirs))
++        outFasta = [z for z in map(gconFunc, outDirs) if z]
+     else:
+         pool = Pool(runner.args.nProcs)
+-        outFasta = filter(lambda z : z, pool.map(gconFunc, outDirs))
++        outFasta = [z for z in pool.map(gconFunc, outDirs) if z]
+ 
+     ## write the results
+     with FastaWriter('/'.join((outDir, "consensus.fa"))) as w:
+@@ -572,7 +572,7 @@ def callConsensus():
+ 
+     ## optionally cleanup
+     if not runner.args.keepTmpDir:
+-        for barcode, reads in readAndReads.items():
++        for barcode, reads in list(readAndReads.items()):
+              bcdir = '/'.join((outDir, barcode))
+              shutil.rmtree(bcdir)
+         
+--- a/tests/cram/consensus.t.disabled
++++ b/tests/cram/consensus.t.disabled
+@@ -1,6 +1,6 @@
+-  $ export INH5=`python -c "from pbcore import data ; print data.getCmpH5()"`
+-  $ export INBH51=`python -c "from pbcore import data ; print data.geBasH5s[0]"`
+-  $ export INBH52=`python -c "from pbcore import data ; print data.getBasH5s[1]"`
++  $ export INH5=`python3 -c "from pbcore import data ; print data.getCmpH5()"`
++  $ export INBH51=`python3 -c "from pbcore import data ; print data.geBasH5s[0]"`
++  $ export INBH52=`python3 -c "from pbcore import data ; print data.getBasH5s[1]"`
+   $ export BARCODE_FASTA=$TESTDIR/../../etc/barcode.fasta
+   $ echo $INBH51 > bas.fofn
+   $ echo $INBH52 >> bas.fofn
+--- a/tests/cram/sanity.t
++++ b/tests/cram/sanity.t
+@@ -1,6 +1,6 @@
+-  $ export INH5=`python -c "from pbcore import data ; print data.getCmpH5()"`
+-  $ export INBH51=`python -c "from pbcore import data ; print data.getBasH5s()[0]"`
+-  $ export INBH52=`python -c "from pbcore import data ; print data.getBasH5s()[1]"`
++  $ export INH5=`python3 -c "from pbcore import data ; print data.getCmpH5()"`
++  $ export INBH51=`python3 -c "from pbcore import data ; print data.getBasH5s()[0]"`
++  $ export INBH52=`python3 -c "from pbcore import data ; print data.getBasH5s()[1]"`
+   $ export BARCODE_FASTA=$TESTDIR/../../etc/barcode.fasta
+   $ echo $INBH51 > bas.fofn
+   $ echo $INBH52 >> bas.fofn

debian/patches/series

 format-manpage.patch
 module-multiarch-path.patch
 spelling.patch
+2to3.patch

debian/rules

@@ -9,12 +9,12 @@ include /usr/share/dpkg/default.mk
 PYBUILD_NAME = pbbarcode
 
 %:
-	LC_ALL=C.UTF-8 dh $@ --with python2 --buildsystem=pybuild
+	LC_ALL=C.UTF-8 dh $@ --with python3 --buildsystem=pybuild
 
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	PYBUILD_SYSTEM=custom \
-	PYBUILD_TEST_ARGS="find tests -name '*.py' | xargs nosetests -v" \
+	PYBUILD_TEST_ARGS="find tests -name '*.py' | xargs nosetests3 -v" \
 	dh_auto_test
 endif
 

debian/tests/control

 Tests: run-unit-test
-Depends: @, pbh5tools, python-nose, python-cram
+Depends: @, pbh5tools, python3-nose, python3-cram
 Restrictions: allow-stderr

debian/tests/run-unit-test

@@ -2,15 +2,15 @@
 
 pkg=pbbarcode
 
-if [ "$ADTTMP" = "" ] ; then
-  ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
-  trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+  AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+  trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
 fi
 
-cp -a /usr/share/doc/${pkg}/etc $ADTTMP
-cp -a /usr/share/doc/${pkg}/tests $ADTTMP
+cp -a /usr/share/doc/${pkg}/etc $AUTOPKGTEST_TMP
+cp -a /usr/share/doc/${pkg}/tests $AUTOPKGTEST_TMP
 
-cd $ADTTMP
+cd $AUTOPKGTEST_TMP
 find . -name "*.gz" -exec gunzip \{\} \;
 
 find tests -name "*.py" | xargs nosetests
@@ -22,8 +22,8 @@ find tests/cram -name "*.t" | grep -v consensus.t | xargs cram --verbose
 
 # I have tried the very first part of this test which translates to
 cd etc
-python -c "from pbcore import data ; print data.getBasH5s()[0]" > bas.fofn
-python -c "from pbcore import data ; print data.getBasH5s()[1]" >> bas.fofn 
+python3 -c "from pbcore import data ; print data.getBasH5s()[0]" > bas.fofn
+python3 -c "from pbcore import data ; print data.getBasH5s()[1]" >> bas.fofn 
 pbbarcode labelZmws barcode.fasta  bas.fofn
 # and even this takes long enough that I decided to kill the process
 # So probably this is nothing we should push to the autopkgtest infrastructure

debian/upstream/metadata

@@ -5,3 +5,5 @@ Registry:
   Entry: OMICS_18566
 - Name: SciCrunch
   Entry: NA
+Repository: https://github.com/PacificBiosciences/pbbarcode
+Repository-Browse: https://github.com/PacificBiosciences/pbbarcode