[BULK] Fix bulk (#12695)

* Update intarna to 2.3.1 (#12367)

* Update agfusion to 1.231 (#12366)

* Update bioconda-utils to 0.15.0 (#12359)

* Update mapdamage2 to 2.0.9 (#12358)

* Update scanpy to 1.3.4 (#12357)

* Update goatools to 0.8.11 (#12361)

* Update perl-math-random-mt-auto to 6.23 (#12362)

* Update kipoi to 0.6.3 (#12374)

* Update kipoi_veff to 0.2.1 (#12364)

* Update perl-object-insideout to 4.05 (#12380)

* Update sevenbridges-python to 0.17.1 (#12379)

* Update nanosv to 1.2.3 (#12378)

* Update starfish to 0.0.30 (#12368)

* Update clust to 1.8.10 (#12356)

* Update pypairs to 2.0.6 (#12381)

* Update khmer to 3.0.0a2 (#12360)

* Update flashlfq to 0.1.110 (#12385)

* Update perl-algorithm-cluster to 1.57 (#12384)

* Update arvados-python-client to 1.2.0.20181121194423 (#12382)

* Update avro-cwl to 1.8.9 (#12355)

* Update avro-cwl to 1.8.9

* Set noarch: python

* r-breakaway (#12386)

* R sads (#12388)

* Update python-sortedcontainers to 2.1.0 (#12383)

* r-ebimetagenomics (#12339)

* pin armadilo on major version (#12389)

* IgDiscover version 0.11 (#12351)

* IgDiscover version 0.11

* IgDiscover requires Python 3.6

* Fix build on macOS with a small patch

* Remove unneeded host dependencies

* Update goatools to 0.8.12 (#12391)

* Update bioconda-utils to 0.15.1 (#12390)

* R ebimetagenomics (#12393)

* Add dimspy recipes for reference purposes (#12387)

* Add dimspy recipes for reference purposes

* Remove filename

* remove from blacklist

* Update build-fail-blacklist

* Added BioExcel_SeqQC to bioconda-recipes (#12276)

* PacBio: Update pbalign to 0.3.2 (#12396)

* PacBio: Update pbalign to 0.3.2

Closes: PacificBiosciences/pbbioconda#39

* add bgreat to bioconda (#12350)

* bgreat addition

* zlib in build should not be needed

* btrim integration to conda (#12395)

* Format sleuth recipe. Trigger rebuild because latest version was never uploaded for some reason. (#12399)

* PacBio: Update `pbsv2` to version 2.1.0 (#12400)

* Genenotebook v0.1.11 (#12398)

* genenotebook recipe

* About

* Package name

* License

* sha256sum

* Update build.sh

* Make bin dir

* Change ln to cp

* New symlink strategy

* Build from prebundled tarball

* genenotebook v0.1.2

* version fix

* retry

* fix

* build number

* genenotebook v0.1.3

* genenotebook v0.1.3

* new build procedure

* change run dependencies

* build

* restore build procedure

* Fix summary

* dependency versions

* v0.1.5

* version fix

* v0.1.6

* reset build number

* build number

* genenotebook v0.1.7

* v0.1.8

* v0.1.9

* v0.1.10

* v0.1.11

* prosolo: new package version 0.6.0 (#12397)

* Update sevenbridges-python to 0.17.2 (#12404)

* Add recipe for ICED (#12406)

* Downgrade version for iced (#12409)

* Update recipe for libstatgen 1.0.5 (#12348)

* Add recipe for libstatgen-1.0.5

* Update iced to 0.5.0 (#12411)

* Update perl-test2-suite to 0.000116 (#12412)

* fix compatibility with other tools (#12415)

* Restore dexseq python helper scripts (#12352)

* Restore dexseq python helper scripts

* Add python requirement for helper scripts

* Add python noarch to build section

* pin it to python2k

* Add htseq requirement, support only python <3 for now

* Genenotebook v0.1.12 (#12418)

* genenotebook recipe

* About

* Package name

* License

* sha256sum

* Update build.sh

* Make bin dir

* Change ln to cp

* New symlink strategy

* Build from prebundled tarball

* genenotebook v0.1.2

* version fix

* retry

* fix

* build number

* genenotebook v0.1.3

* genenotebook v0.1.3

* new build procedure

* change run dependencies

* build

* restore build procedure

* Fix summary

* dependency versions

* v0.1.5

* version fix

* v0.1.6

* reset build number

* build number

* genenotebook v0.1.7

* v0.1.8

* v0.1.9

* v0.1.10

* v0.1.11

* v0.1.12

* updated source

* added medpy recipe (#12417)

* added medpy recipe

* removed osx from build

* Update meta.yaml

* Update meta.yaml

* add boost and a compiler

* Update meta.yaml

* Update meta.yaml

* add itk

* Updated ddrage to version 1.6.1. (#12421)

* Add r-mcpcounter recipe.  (#12261)

* Add MCPcounter recipe.

* fix lint: remove 'fn'

* fix license_file, version number and doi

* Update DEXSeq requirements to force compatible HTSeq version (#12423)

* ARB: Pin glib (#11782)

* Pin glib

* Update meta.yaml

* Update meta.yaml

* Work around CB3 issues

* Work around bioconda-utils lint false positive

* Disable lint check should_not_be_noarch

* Can't reference other packages built in recipe from anything but run

* Move perl to host section. Maybe that helps.

* constraining interpreter version breaks with CB3?

* disable perl version constraint :(

* Update meta.yaml (#12426)

* stacks: fix for fix 'fixing' @ in exe_path (#12420)

* stacks: fix for fix 'fixing' @ in exe_path

the previous fix #11580
tried to solve the problem with the @ in the exe_path by setting this
variable empty. But the perl scripts
- append a / to the empty string and (i.e. the bin path gets /binary)
- check for file presence (problem: neither binary nor /binary are
  present)

Now I quote the @ in the exe_path.

* stacks: add refmap bugfix

* Genenotebook v0.1.13 (#12424)

* genenotebook recipe

* About

* Package name

* License

* sha256sum

* Update build.sh

* Make bin dir

* Change ln to cp

* New symlink strategy

* Build from prebundled tarball

* genenotebook v0.1.2

* version fix

* retry

* fix

* build number

* genenotebook v0.1.3

* genenotebook v0.1.3

* new build procedure

* change run dependencies

* build

* restore build procedure

* Fix summary

* dependency versions

* v0.1.5

* version fix

* v0.1.6

* reset build number

* build number

* genenotebook v0.1.7

* v0.1.8

* v0.1.9

* v0.1.10

* v0.1.11

* v0.1.12

* updated source

* v0.1.13

* metaQuantome (#12413)

replaces metaquant, which is now deprecated.

* New MMseqs2 release 7-4e23d (#12432)

New mmseqs2 release 7-4e23d

* update spades to 3.13.0 (#12408)

* update spades to 3.13.0

* spades: removed dipspades; added 3.12.0 recipe in subdir

* bumped build number for 3.11.1 due to CI failure

* Update Crossmap to 0.3.1 (#12439)

* Update Crossmap to 0.3.1

* Make metaquantome dependencies more specific (#12442)

* less stringent deps

* bump build

* pin goatools

* test extra pins

* integration of bcool to bioconda (#12422)

* Update hifive to 1.5.7 (#12433)

* Update scvi to 0.2.3 (#12434)

* Update Subread from 1.6.2 to 1.6.3. (#12425)

* Update Subread from 1.6.2 to 1.6.3.

* Subread executable coverageCount has been removed.

https://groups.google.com/d/msg/subread/Au1CpKGAXaA/KndhDbrfAwAJ

* UCSC Cell Browser 0.4.23 (#12347)

* Starting files for ucsc-cell-browser

* Customised recipe for ucsc-cell-browser

* meta update for ucsc-cell-browser

* Changes cbTrackHub to cbHub

* Point to static release

* Moves to 0.25

* Updates sha hash for ucsc-browser

* Reverts to 0.1.9

* At ebi

* Update meta.yaml

* pins numpy to last know working version

* Back to 0.25, no numpy pinning.

* Remove git, pin python and numpy. Add build section.

* Update meta.yaml

* Update meta.yaml

* Move to 0.4.20 without skeleton on provisional commit

* Typo on executable name

* Moves to release version and adds dependencies for converters

* Update libstatgen to 1.0.14 (#12437)

* Update arvados-python-client to 1.2.1 (#12438)

* Update tirmite to 1.1.3 (#12435)

* Bump metaquantome (#12449)

* less stringent deps

* bump build

* pin goatools

* test extra pins

* bump metaquantome to 0.99.3

* Update ADAM to 0.25.0 (#12445)

* Update: bcbio, bcbio-vm with viral QC, Docker fixes (#12453)

* update rgi4.2.2 recipe (#12282)

* update to enforce python3.6 and load card.json

* remove lines from build.sh

* update build number

* make PR comment changes

* add test to verify db is loaded

* update build script

* update build script

* fix lint errors

* fix linting errors

* fix liniting errors

* fix linting errors

* fix linting errors

* fix linting errors

* fix linting errors

* fix linting errors

* fix linting errors

* fix linting errors

* fix linting errors

* revert test change

* Add CRAN R package leapp. (#12428)

* Bump DECIPHER to Bioconductor 3.7 (#12463)

* Bump DECIPHER to Bioconductor 3.7

* Change r-rsqlite version dependency

* Update meta.yaml

* updated scVI to 0.2.3 (#12429)

* Add recipe for PyAAVF 0.1.0 (#12451)

* Add recipe for PyAAVF 0.1.0

* Fix linting error

* seqkit 0.9.3 (#12455)

* HTSeq - Pin numpy version (#12467)

* update eigensoft to 7.2.1 (#12469)

* Update scnic to 0.6.0 (#12436)

* Update scnic to 0.6.0

* Work around fastspar insufficient armadillo pin

* fix pin

* GimmeMotifs 0.13.1 (#12471)

* Bumped version to newest, with introspective text (#12461)

* Update Segway 2.0.2 recipe to use older depedencies (#11803)

* Update Segway 2.0.2 recipe to use older depedencies

* Update maximum genomedata version supported

* Update build number

* Fix missing older dependency information

* Update meta.yaml

* updating dependencies for reparation_blast (#12443)

* updating dependencies for reparation_blast

* changed dependency of pysam

* Added DropletUtils package (#12448)

* Create recipe for SVIM (#12272)

* add svim recipe

* fix bugs in svim recipe

* replace source file

* remove license file

* Lowercase biopython

* upgrade to svim 0.4.1

* add GPL LICENSE file, allow python 3.6.* patch releases, add minimap2 dependency

* fix python version

* try to fix lint error

* replace "skip: True" with "noarch: python"

* Update bioconductor-biocgenerics (#12477)

* [X] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html).
* [ ] This PR adds a new recipe.
* [ ] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)).
* [X] This PR updates an existing recipe.
* [ ] This PR does something else (explain below).

* Irida sistr results 0.6.0 (#12478)

* Update irida-sistr-results to 0.6.0

* Fixed dependency string

* Adding recipe for clinvar-tsv v0.1.0. (#12481)

* no fixed boost version (#12483)

* New recipe: pysradb (#12470)

* Pyseer 1.2.0 (#12444)

* Update pyseer to 1.1.2

* Update pyseer to 1.2.0

* Update pyseer to 1.2.0

Update pyseer to 1.2.0

Update pyseer to 1.2.0 (fixed)

* Final touches to pyseer 1.2.0

* Additional update to pyseer recipe

* sentieon: minor version bump to 201808.01 (#12480)

* adding java to mutations recipe (#12485)

* Update ncrf to 1.00.06 (#12369)

* Update ncrf to 1.00.06

* Update test string

* Bump umitools (#12486)

* Mob suite version 1.4.9 no arch build number 2 (#12479)

* Updated to version 1.4.9

* Downgraded to python >= 3.4 to accomodate lowandrew request

* new build

* no arch commit for python 3.4

* no arch conda package version

* Set build number to 1

* Update r-goeveg to 0.4.2 (#12375)

* Update r-goeveg to 0.4.2

* Add r-hmisc as dependency

* Removes r-seurat-scripts from blacklisting (#12489)

* Removes r-seurat-scripts from blacklisting

* Unblacklist some non bioconductor packages

* For VarDict-Java, install utility scripts. (#12488)

* For VarDict-Java, install utility scripts.

Utility script that were previously only shipped with VarDict are not
part of VarDict-Java as well, making installation of both packages
unnecessary.

* Bump build.

* Improve variable name.

* Make vardict depend on vardict-java for utility scripts.

* Pin compatible numpy for older HTSEQ versions (#12490)

* Pin compatible numpy for older HTSEQ versions

This is required to keep older versions of HTSEQ functional

* HTSeq - update old versions to build properly with new build system

* HTSeq 0.6.1 - Increment build number

* add recipe for r-epic (#12473)

* Add new recipe - RVTESTS (#12465)

* Add rvtests

* Update pre-req

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update build.sh

* Update build.sh

* Update build.sh

* Update build.sh

* Update build.sh

* Update build.sh

* Update meta.yaml

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update build.sh

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Create LICENSE

* Update meta.yaml

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update build.sh

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update build.sh

* Create run_test.sh

* Update meta.yaml

* Delete run_test.sh

* Update build.sh

* Update meta.yaml

* Update build.sh

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update build.sh

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update build.sh

* Update build.sh

* Update build.sh

* Update meta.yaml

* Update meta.yaml

* Update build.sh

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Adding recipe for var-agg v0.1.0 (#12482)

* Adding recipe for var-agg v0.1.0

* runtime deps do have run-exports defined

* move rust into the host section

* Adding dependency to clangdev

* Adding var-agg v0.1.1. (#12495)

* [WIP] Salmon v0.12.0 --- try to fix OSX build for real (#12441)

Salmon v0.12.0 --- version bump and fix OSX build

* Considerable updates in terms of features and fixes (check release notes).
* Fix OSX build that would compile, but segfault in quant (but only when built on "old" OSX).

* Performancean alytics (#12498)

* Add bioconductor package RNASeqR

* Add performanceanalytics

* Performancean alytics (#12499)

* Add bioconductor package RNASeqR

* Add performanceanalytics

* Move recipes/r-performanceanalytics and add r-rafalib

* Move r-performanceanalytics/ to recipes

* Update recipes/r-performanceanalytics

* Update r-rafalib

* Remove recipes/r-performanceanalytics/bld.bat

* Remove recipes/r-performanceanalytics

* Update r-performanceanalytics/

* Update r-performanceanalytics/

* Add r-performanceanalytics/

* remove r-performanceanalytics

* Add performanceanalytics

* Remove r-performanceanalytics

* Update Picard to 2.18.20. (#12501)

* Update vsearch to 2.10.0. (#12504)

* Update Purge Haplotigs to v1.0.4 (#12497)

* Update duphold to 0.1.1 (#12516)

* Update starfish to 0.0.31 (#12515)

* Update perl-term-app-roles to 0.02 (#12512)

* Update perl-dbd-sqlite to 1.60 (#12511)

* Update perl-json to 4.00 (#12509)

* Update kipoi to 0.6.5 (#12508)

* Update illumina-interop to 1.1.8 (#12507)

* Update beagle-lib to 3.1.2 (#12523)

* Update pysradb to 0.3.0 (#12522)

* Update bioconda-utils to 0.15.2 (#12525)

* Update perl-json-pp to 4.0 (#12524)

* Update perl-term-table to 0.013 (#12529)

* Update abyss to 2.1.5 (#12528)

* Update perl-test2-suite to 0.000117 (#12527)

* Update wtforms-alchemy to 0.16.8 (#12505)

* Update perl-carp-clan to 6.07 (#12518)

* Update perl-date-manip to 6.75 (#12519)

* Update: seq2c, multiqc-bcbio (#12533)

* tracy v0.3.7 (#12534)

* Version bump 2.10 (#12535)

* Version bump 2.10

* Copy paste error forgot the https

* Missing deps for ucsc-cell-browser 0.4.23 (#12537)

* Missing deps for ucsc-cell-browser

* Bumps build nuber

* Update vsearch to 2.10.1 (#12540)

* New recipe for MicroHapDB 0.2 (#12531)

* New recipe for MicroHapDB 0.2

* Troubleshoot config

* Successful build locally!

* Clean up recipe

* Update moff to 2.0.2 (#12539)

* Update PopDel to version 1.0.5 (#12502)

* Update PopDel to version 1.0.5

* Remove Makefile.patch

Remove Makefile.patch and adapt build.sh to set the correct version, date and CXX-path in its stead.

* Automatically get version from PKG_VERSION

* Update to teloclip v0.0.3 (#12542)

* Update biolite to 1.2.0 (#12544)

* Update kneaddata to 0.7.2 (#12543)

* snakemake 5.3.1 (#12500)

* snakemake 5.3.1

* fix jinja variables

* only warn if git not present in tests

* use explicit jinja for version again.

Conda seems to have lost the ability to use PKG_VERSION in meta.yaml.

* try masking env var

* try defining env var before command

* nextflow: pin openjdk=8 to solve java version parsing issue (#12493)

* Pin openjdk=8

* Alllow openjdk 8 or 9

* Update bioconda-utils to 0.15.3 (#12546)

* Update: mosdepth (0.2.4) bcbio/bcbio-nextgen#2590 (#12549)

* Update: mosdepth (0.2.4) bcbio/bcbio-nextgen#2590

* Update install patch for 0.2.4

* Match nim release version 0.19.0

* Scanpy scripts (#12551)

* Bump version

* Fix scanpy version requirement to v1.3.2

* Update to v0.0.4

* Update nanosim to 2.2.0 (#12517)

* Update nanosim to 2.2.0

* Add sklearn as dependency

* Recipe for kma (#12554)

* PacBio: Update `pbsv2` to version 2.1.1 (#12556)

* Add counterr (#12541)

* Add counterr

* Fix typo

* Use tagged release

* Updated ddRAGE to version 1.6.3 (#12557)

* Add recipe for SNVer 0.5.3 (#12265)

* Add recipe for SNVer 0.5.3

* Add CRAN R package cate. (#12562)

* r-seurat-scripts: Fixed DimPlots() issues, addressed libpng issue for OSX (#12563)

* Fixed DimPlots() issues, addressed libpng issue for OSX

* Correction: removed testing line in source package

* Update scanpy to 1.3.5 (#12571)

* Update vsearch to 2.10.2 (#12579)

* Update mentalist to 0.2.4 (#12578)

* Update krakenuniq to 0.5.5 (#12575)

* Update mlst to 2.16 (#12572)

* Update transit to 2.3.3 (#12570)

* Update anndata to 0.6.14 (#12568)

* Update svim to 0.4.2 (#12566)

* Update perl-test-cleannamespaces to 0.24 (#12569)

* uptdate mlst to 2.16.1 (#12582)

* Update jcvi to 0.8.12 (#12574)

* add cromwell-tools (CLI and API for Cromwell workflow manager). (#12564)

* added cromwell-tools

* point to stable docs rather than latest

* Remove noarch to make os-specifics work (#12583)

* prosolo: update to v0.6.1 (#12584)

* integration to bioconda (#12456)

* Recipe for sparcc (#12459)

* Recipe for SparCC

* Remove maintainers lines

* Add license info

* Mention pull request for patch

* Fix lint

* Build noarch

* Update: bcbio (v1.1.2), bcbio-vm (GCP support) (#12585)

* t-coffee 12.00.7fb08c2 (#12594)

* t-coffee 12.00.7fb08c2

* add viennarna to deps

Adding viennarna to runtime dependencies will include RNAplfold thus allowing -mode rcoffee to run.

* t-coffee 12.00.7fb08c2 (2)

This commit adds vienna packages
and remove TMalign copy command

* t-coffee 12.00.7fb08c2 (4)

Adding TMalign

* Nf core V 1.4  (#12599)

* Need to update SHA256 once release is out!

* Update to release 1.4

* Sleuth unblacklist (#12591)

* remove sleuth from blacklist

* Remove obsolete dependency.

* Bump spectra-cluster-cli (#12598)

* Update gseapy to 0.9.9 (#12530)

* Update gseapy to 0.9.9

* Add scipy

* Add bioservices as dependency

* added recipe perl-bio-viennangs 0.19.2 (#12596)

* Add SVMlight  (#12595)

* Add SVMlight

* Update meta yaml

* Update SHA256 sum

* Update build script to copy executables

* Update meta.yaml

* Fix o-umlaut

* Fix test stalls

svm_learn -? displays a pager, waiting for keyboard input

* rhdf5 2.26 and rhdf5lib 1.4 (#12597)

* rhdf5 2.26 and rhdf5lib 1.4

* force C99 mode

* set CFLAGS in Makevars

* Add recipe for hiddenDomains (#12614)

* bump pysradb 0.3.0 -> 0.4.0 (#12612)

* bump pysradb 0.3.0 -> 0.4.0

* Fix imports

* Add extras

* Update slicedimage to 1.0.2 (#12609)

* Update perl-module-scandeps to 1.26 (#12608)

* Update scanpy to 1.3.6 (#12605)

* Update abeona to 0.40.2 (#12602)

* Update confindr to 0.4.8 (#12607)

* Update anndata to 0.6.15 (#12606)

* tmaling (#12588)

Add tmalign recipe

* pysvmlight added (#12617)

* Add fontconfig / ttf-dejavu to fastqc recipe (#12616)

* pdate adVNTR to 1.2.0 (#12613)

* add adVNTR

* fix linux error for adVNTR

* add numpy to adVNTR requirements

* add numpy include dirs for cythonize

* Update advntr to 1.1.0

* Update advntr to 1.1.0

* update advntr to 1.1.1

* update adVNTR to 1.2.0

* update sha256 for adVNTR-1.2.0

* fix build script for adVNTR-1.2.0

* fix adVNTR-1.2.0

* PeptideShaker v1.16.36 & SearchGUI v3.3.10 (#12620)

* PeptideShaker updated to v1.16.32
SearchGUI updated to v3.3.6

* PeptideShaker updated to v1.16.35

* SearchGUI updated to v3.3.9

* PeptideShaker version updated to 1.16.36
SearchGUI version updated to 3.3.10

* New recipe (refinem: 0.0.24) (#12628)

* Replace sha256 and bump build num (#12629)

* Update galaxy-parsec to 1.0.6 (#12634)

* Add recipe for SeqMap (#12615)

* Add recipe for SeqMap

* Change cp

Change cp

* Updated concoct to version 1.0.0 (#12600)

* Updated concoct to version 1.0.0

* Skip build for macosx at this point

* New build number

* Reset build number to 0, thanks @druvus

* Update deepvariant to 0.7.2 (#12638)

* Update abeona to 0.41.1 (#12637)

* Update shmlast to 1.3 (#12636)

* Update krakenuniq to 0.5.6 (#12633)

* Update selene-sdk to 0.2.0 (#12632)

* Update comet-ms to 2018013 (#12555)

* Update with selene-sdk v0.2.0 (#12631)

* update with selene-0.2.0

* Update meta.yaml

* add self to recipe maintainers

* Cat updated version (#12587)



* v 4.3.1

* Pin BLAST+ version to >= 2.2, < 2.4 (#12639)

* Shmlast v1.4 (#12645)

* Bump shmlast to v1.4

* Update PopDel to version 1.0.6 (#12644)

* Update PopDel to version 1.0.6

* Adapt tests

* Remove test for correct version number

Redirection seems to cause error in circleci:
".Passing program arguments as a string may be a security hazard if combined with untrusted input"

* Concoct add samtools as a dependency (#12642)

* Updated concoct to version 1.0.0

* Skip build for macosx at this point

* New build number

* Reset build number to 0, thanks @druvus

* Samtools new requirement for concoct v1.0.0

* Bump topas (#12618)

* Bump spectra-cluster-cli

* Bump topas

* Use ${PKG_VERSION}

* Small tweaks

* No recursion

* pasta-1.7.8-build-2 (#12641)

* pasta-1.7.8-build-2

* Relax requirements

* Rebuild pasta (#12648)

* Bump spectra-cluster-cli

* Delete old pasta

* Rebuild pasta

* Unblacklist pasta

* Revert dendropy version

* Correct build number

* Use openjdk

* Rebuild perl-pod-coverage (#12652)

* Rebuild perl-pod-coverage

* Unblacklist

* tracy v0.3.8 (#12651)

* Kalign (#12647)

* add kalign

This recipe adds kalign

* fix for osx

* fix for osx #2

* Rebuild perl-test-pod-coverage (#12654)

* Rebuild perl-test-pod-coverage

* Unblacklist

* Update: bcbio (1.1.3a) Fixes bcbio/bcbio-nextgen#2594 (#12655)

* Rebuild perl-test-file-contents (#12649)

* Bump spectra-cluster-cli

* Rebuild perl-test-file-contents

* Kleborate 0.3.0 (#12657)

* Adding recipe for >> kleborate <<

* Rebuild perl-params-coerce (#12660)

* Upgrade biodb to version 1.2.0b. (#12663)

* Add recipe for unitas (#12658)

* Add recipe for unitas

* Rebuild perl-file-share (#12661)

* Update sevenbridges-python to 0.17.3 (#12667)

* Update slicedimage to 1.0.3 (#12666)

* Update cat to 4.3.3 (#12665)

* Update crossmap to 0.3.2 (#12664)

* Update: deepvariant 0.7.2 model and dependencies (#12672)

- Requires tensorflow 1.12
- Update model data for 0.7.2
- Remove requirement for --regions in dv_make_examples.py wrapper. Fixes #12560

* unblacklist perl-bio-viennangs (#12643)

* unblacklist perl-bio-viennangs

* fix version string; remove 0.19 recipe

* remove all perl version strings

* increased build nr

* Add pysvmlight (#12673)

* Remove the mess I created in the main repository (#12674)

* Add missing dependencies and bump version for FRED2 (#12621)

* Add missing dependencies and bump version for FRED2

* Bump version to force rebuild

* Update meraculous to 2.2.6 (#12254)

* Update meraculous to 2.2.6

* Remove perl pinning

* Update BioExcel_SeqQC to 0.6 (#12604)

* Update BioExcel_SeqQC to 0.6

* Fix name

* Update anndata to 0.6.16 (#12676)

* Update pysradb to 0.4.2 (#12675)

* version 3.0.3 (#12678)

* Add perl-math-utils (#12681)

* Add perl-math-utils

* Remove fn

* Rebuild perl-extutils-makemaker (#12680)

* Update perl-html-formatter to 2.16 (#12225)

* Update perl-html-formatter to 2.16

* Fix deps

* Update perl-readonly to 2.05 (#12153)

* Update perl-readonly to 2.05

* Fix deps

* Update perl-html-tidy to 1.60 (#12187)

* Update perl-html-tidy to 1.60

* Update deps

* Update meta.yaml

* Update perl-libwww-perl to 6.36 (#12180)

* Update perl-libwww-perl to 6.36

* Update deps

* Update meta.yaml

* Add perl-html-parser as dep

* Add back perl-ntlm

* Update PopDel to version 1.0.7 (#12685)

* Use quotes when extending PATH. (#12662)

* Use quotes when extending PATH env var, in order to handle potential space characters.

* Update perl-math-derivative to 1.01 (#12158)

* Update perl-math-derivative to 1.01

* Update dependency

* Update perl-data-dumper to 2.173 (#12224)

* Update perl-parallel-forkmanager to 2.02 (#12170)

* Update perl-parallel-forkmanager to 2.02

* Update deps

* Update bioblend to 0.12.0 (#12687)

* Update abeona to 0.42.0 (#12686)

* blacklist r-rbamtools

build-fail-blacklist

@@ -116,6 +116,7 @@ recipes/r-propcis
 recipes/r-purbayes
 recipes/r-qiimer
 recipes/r-qtl
+recipes/r-rbamtools
 recipes/r-rcircos
 recipes/r-readbrukerflexdata
 recipes/r-readmzxmldata