# ----- 2023-12-02 problematic on bulk -----

r-ramclustr

# ------------------------------------------

# Currently kills bulk, and dependants

recipes/bioconductor-missmethyl

recipes/bioconductor-conumee

recipes/r-shazam

recipes/r-scoper

recipes/r-dowser

recipes/bioconductor-chipxpressdata

recipes/bioconductor-chipxpress

recipes/bioconductor-meal

recipes/bioconductor-dmrcate

recipes/bioconductor-methylgsa

recipes/bioconductor-champ

recipes/bioconductor-appreci8r

recipes/bioconductor-mirsm

# Allegedly requires ancient gatb

recipes/lordec

# Uses all the RAM/time on github actions

recipes/octopus

recipes/bttcmp

recipes/bttoxin_scanner

recipes/hail

recipes/monocle3-cli

recipes/phenix

recipes/mtsv

# Fills the disk on the CI

recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5

recipes/bioconductor-mafdb.gnomad.r2.1.grch38

recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch37

recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch38

recipes/bioconductor-trena

# x86_64-conda-linux-gnu-cc: error: unrecognized command-line option '-R'

recipes/ncbi-util-legacy

# HDF5 compatibility, https://github.com/mateidavid/nanocall/issues/38

recipes/nanocall

# source code no longer available

recipes/bugseq-porechop

# move to conda-forge

recipes/autolog

recipes/avro-python2

recipes/cityhash

recipes/collectl

recipes/elasticluster

recipes/epydoc

recipes/esmre

recipes/forked-path

recipes/gnuplot-py

recipes/justbackoff

recipes/kid

recipes/myriad

recipes/nose-capturestderr

recipes/pdfkit

recipes/perl-mozilla-ca

recipes/perl-pcap

recipes/perl-getopt-argvfile

recipes/perl-data-dump

recipes/perl-text-csv_xs

recipes/perl-probe-perl

recipes/perl-lwp-protocol-https

recipes/perl-libwww-perl

recipes/perl-test-xml

recipes/perl-www-mechanize

recipes/perl-rest-client

recipes/perl-net-http

recipes/perl-lwp-simple

recipes/perl-soap-lite

recipes/perl-xml-twig

recipes/perl-digest-md5-file

recipes/perl-graphviz

recipes/perl-xml-dom-xpath

recipes/perl-xml-dom

recipes/perl-util-properties

recipes/pyasp

recipes/pyexcelerator

recipes/pyhashxx

recipes/pyopt

recipes/pysvg

recipes/pyx

recipes/rdfextras

recipes/scala

recipes/sharedmem

recipes/stacks_summary

recipes/tgt

recipes/workspace

recipes/wtforms-alchemy

recipes/wtforms-components

recipes/xmlbuilder

# the following packages have open PRs labeled with "Move to conda-forge"

recipes/perl-alien-build

recipes/perl-alien-libxml2

recipes/perl-date-manip

recipes/perl-datetime-timezone

recipes/perl-devel-checklib

recipes/perl-ffi-checklib

recipes/perl-file-sharedir-install

recipes/perl-graphviz

recipes/perl-hpc-runner-command-plugin-logger-sqlite

recipes/perl-html-form

recipes/perl-http-message

recipes/perl-image-info

recipes/perl-ipc-run

recipes/perl-module-corelist

recipes/perl-parallel-iterator

recipes/perl-pdf-api2

recipes/perl-perlio-utf8_strict

recipes/perl-sereal-decoder

recipes/perl-sereal-encoder

recipes/perl-term-progressbar

recipes/perl-uri

recipes/perl-xml-libxml

recipes/scoop

recipes/wheezy.template

# perl package with no proper installation method

recipes/feelnc

# incompatible with htslib >1.10 https://github.com/statgen/popscle/issues/57

recipes/popscle

# Maven no longer accepts http connections https://github.com/rdpstaff/ReadSeq/issues/2

recipes/rdp-readseq

# Only specific versions are failing

recipes/emmix/1.3

recipes/hyphy/2.3.11

recipes/skewer/0.1.126

recipes/blast/2.2.31

recipes/bedtools/2.26.0

recipes/opsin/1.4.0

recipes/opsin/2.1.0

recipes/meme/4.11.1

recipes/meme/4.11.2

recipes/meme/4.8.1

recipes/bcftools-gtc2vcf-plugin/1.9

recipes/panx/1.6.0

recipes/panx/1.5.0

recipes/haploclique/1.3.1

recipes/blast/2.5.0

# Unclear that the following old version is still needed, but the main recipe has an older version?!?

recipes/mira/4.9.6

# need to fix the download location, the checksum changes everytime

recipes/osra/2.1.0

recipes/imfusion/0.3.2

# can't open file setup.py

recipes/meneco/1.5.2

# Permission denied ESTscan

recipes/perl-estscan2/2.1

# Source code no longer easily available

recipes/strip_it/1.0.2

recipes/shape_it/1.0.1

recipes/tqdist/1.0.0

recipes/ocrad/0.21

recipes/perl-estscan1/1.3

recipes/bwa/0.6.2

# reprocessed to here

# fails compilation in bulk on Linux

recipes/paragraph

recipes/selectsequencesfrommsa

recipes/nasp

recipes/mmvc

recipes/gemma

recipes/roary

recipes/deltabs

recipes/gottcha

recipes/pepnovo

recipes/ea-utils

recipes/nextgenmap

recipes/igor_vdj

recipes/pargenes

recipes/porfast

recipes/agg

recipes/hg-color

recipes/bandage

recipes/prosolo

recipes/ratt

recipes/graphclust-wrappers

recipes/swga

recipes/jvarkit-bam2wig

recipes/jvarkit-bam2svg

recipes/jvarkit-msa2vcf

recipes/rxdock

recipes/cath-tools

recipes/phame

recipes/goetia

recipes/consel

recipes/isaac4

recipes/clame

recipes/prosic

recipes/dms

recipes/variant_tools

recipes/translig

recipes/lsc

recipes/rambo-k

recipes/mobster

recipes/visceral-evaluatesegmentation

recipes/chicagotools

recipes/skewer

recipes/trim_isoseq_polya

recipes/ra/ra-assembler

recipes/pureclip

recipes/hulk

recipes/bolt-lmm

recipes/unitig-counter

recipes/probcons

recipes/spydrpick

recipes/bctools

recipes/bayestyper

recipes/group_humann2_uniref_abundances_to_go

recipes/isonclust2

recipes/sibelia

recipes/var-agg

recipes/wham

# Segfaults in bulk on Linux 24.3.2021

recipes/dbgraph

recipes/mira

# Source code moved

recipes/astalavista

recipes/kggseq

recipes/hts-nim-tools

recipes/oligoarrayaux

recipes/coral

recipes/ngsep

recipes/rnabridge-denovo

recipes/eval

recipes/minorseq

recipes/methylextract

recipes/blasr

recipes/asn2gb

recipes/orfm

recipes/maaslin

recipes/seqmap

recipes/micropita

recipes/assemblytics

recipes/nemo

recipes/pblaa

recipes/translatorx

recipes/meme/4.11.1

recipes/meme/4.8.1

recipes/bax2bam

recipes/break-point-inspector

recipes/embl-api-validator

recipes/readseq

recipes/smcounter2

recipes/compalignp

recipes/reaper

recipes/genie

recipes/admixture

recipes/mace

recipes/riboseq-rust

# vendors bzip2, samtools, etc.

recipes/rvtests

# Source URL no longer exists

recipes/python-mailund-newick

recipes/piret

# Requires obsolete matplotlib versions incompatible with our gfortran pinnings

recipes/riboplot

# Requires libXext.so.6 in the container

recipes/samsifter

# Mulled test never completes

recipes/comparative-annotation-toolkit

# compilation or other errors in bulk

recipes/transcomb

recipes/detonate

recipes/bmtagger

# Killing bulk

recipes/rsat-core

# Packages failing in bulk that haven't yet received more attention

recipes/ig-checkflowtypes

recipes/bufet

recipes/mapsplice

recipes/halla

recipes/qtip

recipes/tagger

recipes/compare-reads

recipes/strainest

recipes/t_coffee

recipes/shannon_cpp

recipes/ecopy

recipes/qiimetomaaslin

recipes/groopm

recipes/biolite

recipes/pauda

recipes/hicbrowser

recipes/vqsr_cnn

recipes/bam-readcount

recipes/mqc

recipes/roprofile

recipes/chanjo

recipes/phylip

recipes/gqt

recipes/diamond_add_taxonomy

recipes/shapemapper

recipes/rnftools

recipes/embassy-phylip

recipes/triform2

recipes/lcfit

recipes/tadarida-c

recipes/w4mclstrpeakpics

# KeyError: '>=1.0.6'

# (apparently due to bzip2 constraint)

recipes/sgcocaller

recipes/sscocaller

# numba import fails with no exception

recipes/sparse-neighbors-search

# needs specific clusterprofiler and enrichplot versions that are not currently available

recipes/vsclust

# having issues compiling on macOS

recipes/circle-map-cpp

# make: common": No such file or directory

recipes/conduit-assembler

# configure: error: cannot find required auxiliary files: config.guess config.sub

recipes/bcftools-snvphyl-plugin

# rnamoves.c:(.text.RNA2_move_noLP_bpshift+0x1f): undefined reference to `close_bp'

recipes/kinsimriboswitch

# configure: error: R package gtools not found.

# (even though r-gtools is in host: and run:

recipes/footprint

# Requests python3, but is written for python2

recipes/ctat-mutations

# Seems to download maven and then have java issues

recipes/megagta

# Unknown issues

recipes/cmv

recipes/fwdpp

recipes/parafly

recipes/smashbenchmarking

recipes/saffrontree

recipes/slclust

# tracking master branch

recipes/frc

# CMake Error at build-common/cmake/VersionHelper.cmake:11 (list):

recipes/somatic-sniper

# can't find file to patch at input line 3

recipes/erds

# non-standard test

recipes/fermikit

# build-error

recipes/mimodd

# error: possibly undefined macro: AM_GNU_GETTEXT

recipes/xcftools

# See https://github.com/bioconda/bioconda-recipes/pull/9458

recipes/spingo

# CMake Error: The source directory "/opt/conda/conda-bld/sqlitebrowser_1529759350498/work" does not appear to contain CMakeLists.txt.

recipes/sqlitebrowser

# no test, website down

recipes/sprinkles

# link not founds

recipes/soapcoverage

# download error

recipes/soapaligner

# missing tarball

recipes/sloika

recipes/genometools

recipes/nanonet

recipes/knot

recipes/jali

recipes/intervalstats

# missing dep

recipes/oligotyping

recipes/oligotyping/2.0

# missing binary

recipes/semeta

# Various C++ errors

recipes/rdock

# WARNING (talloc,lib/libpytalloc-util.so.2.1.9): did not find - or even know where to look for: /lib64/libm.so.6

recipes/talloc

# Skipped: vnl from /opt/recipe defines build/skip for this configuration ({'c_compiler': 'toolchain_c'}).

recipes/vnl

# something wrong with the test

recipes/remurna

# Test uses a program that makes incorrect assumptions about shebangs (you can't reliably use "#!/usr/bin/env program --arguments")

recipes/amos

# aclocal error, but also downloads mauve tarballs, but there is now a mauve pkgs, is it still needed?

recipes/libmuscle

# compilation error

recipes/lightning

# unable to access jarfile

recipes/effectivet3

# url broken

recipes/e-pcr

# linker error

recipes/discovar-denovo

# depends on perl-pcap

recipes/brass

# oh no TPP is failing, it was a nightmare to get it to compile in the first place :(

recipes/tpp

# perl dependency estmapper not available for 5.26

recipes/wgs-assembler

# requires wgs-assembler, which has a build fail

recipes/sprai

# missing dependency

recipes/genomebaser

recipes/garnet

recipes/tablet

# RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml url=https://pypi.org/simple/funcsigs/

recipes/pytest-marks

recipes/hubward

recipes/phylotoast

# git checkout problem

recipes/icqsol

recipes/pout2mzid

# checksum always fails

recipes/ms

# PREFIX/lib is a directory

recipes/proot

# bin/g++: Command not found

recipes/metavelvet-sl

recipes/metavelvet

# cp: target `/opt/conda/conda-bld/meryl_1530057980094/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/' is not a directory

recipes/metavelvet-sl-pipeline

# Conflicting numpy and qiime

recipes/koeken

# cp: cannot stat `./mapsembler2_extremities/build/mapsembler2_extremities': No such file or directory

recipes/mapsembler2

# Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!

recipes/primerprospector

# missing URL

recipes/intemap

# zlib missing

recipes/polymutt

# /opt/rh/devtoolset-2/root/usr/libexec/gcc/x86_64-redhat-linux/4.8.2/ld: cannot find -lc

recipes/piler

# /usr/bin/env: python -Es: No such file or directory

recipes/pizzly

# natsort conflicts with python

recipes/qcumber

# Tests failed for spanki-0.5.1-py27h24bf2e0_1.tar.bz2 - moving package to /opt/conda/conda-bld/broken

recipes/spanki

# broken pipe

recipes/antarna

# hashFunction.c:94: Error: invalid instruction suffix for `push'

recipes/soapdenovo2

# tarball missing and should be migrated I guess

recipes/ngseqbasic

# missing bioc package

recipes/customprodb

# Error: Could not find or load main class edu.duke.igsp.gkde.Main

recipes/fseq

# node error

recipes/azure-cli

recipes/arvados-cli

# takes to long to install

recipes/bcbio-rnaseq

# missing python requirements?

recipes/illuminate

# dotnet not found

recipes/canvas

# perl script could not be found

recipes/rnaclust

# Unknown issues

recipes/lorma

recipes/minialign

recipes/nspdk

recipes/dreamtools

recipes/biomaj

recipes/cas-offinder

recipes/odose

# /opt/conda/conda-bld/pash_1531691261758/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/ruby/2.4.0/rubygems/core_ext/kernel_require.rb:55:in `require': cannot load such file -- brl/util/textFileUtil (LoadError)

recipes/pash

# Uses deprecated POSIX::tmpnam() function, not maintained, partially replaced by estscan 3.0

recipes/perl-btlib/0.19

# takes a long time and then fails?

recipes/kmerinshort

# chmod: cannot access `genblast_v1.0.4': No such file or directory

recipes/genblasta

# ImportError: cannot import name 'aveQual'

recipes/nanosplit

# Error: Unable to access jarfile

recipes/gfinisher

# gsl missing but specified

recipes/gfold

# compilation error, missing boost header

recipes/k-slam

# missing fortran lib, will fix this upstream

recipes/ig-checkfcs

# np-likeness scorer no such file or directory

recipes/np-likeness-scorer

# Throws an error during testing

recipes/reago

# Error during mulled testing on circleci

recipes/ra-integrate

# /boost/intrusive/list.hpp:123:22: error: ‘const bool boost::intrusive::list_impl<boost::intrusive::bhtraits<dng::pileup::Node, boost::intrusive::list_node_traits<void*>, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 1u>, long unsigned int, true, void>::safemode_or_autounlink’ is private

recipes/denovogear

# /opt/rh/devtoolset-2/root/usr/libexec/gcc/x86_64-redhat-linux/4.8.2/ld: cannot find -lboost_system

recipes/metaprob

# Fails testing

recipes/cap-mirseq

recipes/graphprot

# OSX related errors, Linux should be fine. Most of the non-perl issues are due to LLVM used as a compiler, GCC should be fine

recipes/cgat-scripts

recipes/smalt

recipes/oases

recipes/metavelvet-sl-feature-extraction

recipes/music

recipes/kraken-ea

recipes/gnu-getopt

recipes/domclust

recipes/flock

recipes/cmfinder

recipes/cortex_con

recipes/cosi2

recipes/cufflinks

recipes/esimsa

recipes/fastuniq

recipes/fgap

recipes/funcannot

recipes/genepender

recipes/ghostx

recipes/ls-gkm

recipes/mosaik

recipes/mustang

recipes/ngmerge

recipes/nlstradamus

recipes/panoct

recipes/pygresql

recipes/real

recipes/rmap

recipes/rnabob

recipes/sam

recipes/sff2fastq

recipes/snpomatic

recipes/soapdenovo2-gapcloser

recipes/spectral_hk

recipes/swiftlink

recipes/tedna

recipes/transtermhp

recipes/carna

# stringify can't find libmysqlclient.18

recipes/ucsc-overlapselect

recipes/ucsc-pslmap

# Source seems to have moved

recipes/discovar

# source code no longer available at URL

recipes/wade

# Requirements pinned down so much that rebuilds are prevented. (Some old deps may only be available on the old pks/free defaults channel.)

recipes/oncotator

# Depends on rdfextras with depends old pyparsing not available on conda-forge and pkgs/main (only on pkgs/free)

recipes/pacbio_falcon

# Depends on old matplotlib <1.5.0 not available on conda-forge and pkgs/main (only on pkgs/free)

recipes/pymix

# Depends on pymix, see above

recipes/ale

# Pinned to biopython=1.65 which is only availble through pkgs/free. If it doesn't break the package, the requirement should be set to biopython=1.70 or higher.

recipes/breakseq2

# R package build segfaults: [2020-07-28 05:38:00] Plotting genome...\n\n*** caught segfault ***\naddress (nil), cause 'memory not mapped'\n\nTraceback:\n 1: cairoVersion()\n 2: grSoftVersion()\n 3: symbolType1support()\n 4: optionSymbolFont(d$symbolfamily)\n 5: png(paste0(xargs$out, ".cnv.png"), units = "px", width = 1600, height = 1600, res = 300)

recipes/cnv_facets

# Depends on r-base and mentalist. The latter has has pinned down dependencies preventing the installation alongside other packages like r-base. Need to fix mentalist!

recipes/pathogist

# Uses binary wheel that have been deleted upstream (and are not available from depot.galaxyproject.org). To fix it, build from source

recipes/python-consensuscore2

# Pinned to older Bioconductor package version that is not build for current R

recipes/scater-scripts

recipes/sc3-scripts

# Warning: replacing previous import ‘BiocGenerics::combine’ by ‘gridExtra::combine’ when loading ‘RiboseQC’\nWarning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘RiboseQC’\nERROR: lazy loading failed for package ‘RiboseQC’\n* removing ‘$PREFIX/lib/R/library/RiboseQC’\nError: object ‘DEFAULT_CIRC_SEQS’ is not exported by 'namespace:GenomicFeatures'

recipes/riboseqc

# Some UnsatisfiableError

recipes/music-deconvolution

# Bulk times out while solving environment

recipes/mercat

recipes/panpasco

# Needs a bunch of fixes (remove outdated conda-forge::perl workaround, not symlinking compiler/linker, linker fixes, etc.).

recipes/arb-bio

# Source needs patching ("degree()" definition is ambiguous):

# BWTIL/data_structures/../common/../extern/bitvector/include/internal/bitvector.hpp:815:43: error: expression cannot be used as a function

# t.ranks(child, degree()) -= 1;

recipes/erne

# Vendors gsl but fails to compile it.

recipes/rseg

# Uses pyinstaller (why??) but doesn't run: "Cannot open self $PREFIX/bin/taco_run or archive $PREFIX/bin/taco_run.pkg"

recipes/taco

# Unknown issues

recipes/cnvetti

recipes/proteowizard

recipes/bibliospec

# OCaml/opam build fails

recipes/phylocsf

# Ruby build failes

recipes/protk

# Does not link include -lGL -lGLU when linking, might require libOSMesa.

recipes/connectome-workbench

# Build fails during boostrap of vendored Boost.

recipes/gvcftools

recipes/seer

# Can't compile

recipes/gplas

# compilation error and dependants

recipes/mmult

recipes/bioconductor-hilbertvisgui

recipes/bioconductor-travel

recipes/bioconductor-netboost

# some missing perl dependency

recipes/perl-biox-workflow-command

# python 2-only with C requiring graphiv. No longer supportable

recipes/sshmm

# Source code no longer easily available

recipes/cap3

recipes/bumbershoot

recipes/gerp

recipes/turbocor

# tool renamed

recipes/titan-gc

# failing in bulk for now

recipes/cmip

recipes/cesm

recipes/minnow

recipes/quip

recipes/conterminator

recipes/mantis

recipes/apoc

recipes/quorum

recipes/noresm

recipes/xsd

recipes/callstate

recipes/hypo

recipes/pb-falcon-phase

recipes/hiline

recipes/eqtlbma

recipes/barriers

# Requires rmblast update

recipes/maker

# Takes hours to solve the environment

recipes/rop

# Need to redo the skeletons for these

recipes/ucsc-axttomaf

recipes/ucsc-bamtopsl

recipes/ucsc-bedcoverage

recipes/ucsc-bedextendranges

recipes/ucsc-bedintersect

recipes/ucsc-beditemoverlapcount

recipes/ucsc-bedjointaboffset

recipes/ucsc-bedpileups

recipes/ucsc-bedrestricttopositions

recipes/ucsc-bedtopsl

recipes/ucsc-bedweedoverlapping

recipes/ucsc-bigwigmerge

recipes/ucsc-blasttopsl

recipes/ucsc-catdir

recipes/ucsc-catuncomment

recipes/ucsc-chainbridge

recipes/ucsc-chainfilter

recipes/ucsc-chainnet

recipes/ucsc-chainprenet

recipes/ucsc-chainsplit

recipes/ucsc-chainstitchid

recipes/ucsc-chainswap

recipes/ucsc-chaintoaxt

recipes/ucsc-chaintopsl

recipes/ucsc-chaintopslbasic

recipes/ucsc-checkagpandfa

recipes/ucsc-checkcoveragegaps

recipes/ucsc-checkhgfindspec

recipes/ucsc-checktablecoords

recipes/ucsc-chopfalines

recipes/ucsc-chromgraphfrombin

recipes/ucsc-chromgraphtobin

recipes/ucsc-clustergenes

recipes/ucsc-coltransform

recipes/ucsc-countchars

recipes/ucsc-crtreeindexbed

recipes/ucsc-crtreesearchbed

recipes/ucsc-dbsnoop

recipes/ucsc-dbtrash

recipes/ucsc-endsinlf

recipes/ucsc-estorient

recipes/ucsc-expmatrixtobarchartbed

recipes/ucsc-faalign

recipes/ucsc-facmp

recipes/ucsc-facount

recipes/ucsc-fafilter

recipes/ucsc-fafiltern

recipes/ucsc-fafrag

recipes/ucsc-fanoise

recipes/ucsc-faonerecord

recipes/ucsc-fapolyasizes

recipes/ucsc-farandomize

recipes/ucsc-farc

recipes/ucsc-fasize

recipes/ucsc-fasplit

recipes/ucsc-fastqstatsandsubsample

recipes/ucsc-fastqtofa

recipes/ucsc-fatofastq

recipes/ucsc-fatotab

recipes/ucsc-fatrans

recipes/ucsc-featurebits

recipes/ucsc-findmotif

recipes/ucsc-gaptolift

recipes/ucsc-genepredfilter

recipes/ucsc-genepredhisto

recipes/ucsc-genepredsinglecover

recipes/ucsc-genepredtofakepsl

recipes/ucsc-genepredtomafframes

recipes/ucsc-genepredtoprot

recipes/ucsc-gensub2

recipes/ucsc-getrna

recipes/ucsc-getrnapred

recipes/ucsc-gff3topsl

recipes/ucsc-gmtime

recipes/ucsc-headrest

recipes/ucsc-hgbbidblink

recipes/ucsc-hgfakeagp

recipes/ucsc-hgfindspec

recipes/ucsc-hggoldgapgl

recipes/ucsc-hgloadbed

recipes/ucsc-hgloadchain

recipes/ucsc-hgloadmaf

recipes/ucsc-hgloadnet

recipes/ucsc-hgloadout

recipes/ucsc-hgloadoutjoined

recipes/ucsc-hgloadsqltab

recipes/ucsc-hgloadwiggle

recipes/ucsc-hgspeciesrna

recipes/ucsc-hgsqldump

recipes/ucsc-hgtrackdb

recipes/ucsc-hgvstovcf

recipes/ucsc-htmlcheck

recipes/ucsc-hubcheck

recipes/ucsc-hubpubliccheck

recipes/ucsc-lavtoaxt

recipes/ucsc-lavtopsl

recipes/ucsc-ldhggene

recipes/ucsc-liftup

recipes/ucsc-linestora

recipes/ucsc-localtime

recipes/ucsc-mafaddirows

recipes/ucsc-mafaddqrows

recipes/ucsc-mafcoverage

recipes/ucsc-maffetch

recipes/ucsc-maffilter

recipes/ucsc-maffrag

recipes/ucsc-maffrags

recipes/ucsc-mafgene

recipes/ucsc-mafmefirst

recipes/ucsc-maforder

recipes/ucsc-mafranges

recipes/ucsc-mafsinregion

recipes/ucsc-mafspecieslist

recipes/ucsc-mafspeciessubset

recipes/ucsc-mafsplit

recipes/ucsc-mafsplitpos

recipes/ucsc-maftoaxt

recipes/ucsc-maftobigmaf

recipes/ucsc-maftopsl

recipes/ucsc-maftosnpbed

recipes/ucsc-maketablelist

recipes/ucsc-maskoutfa

recipes/ucsc-mktime

recipes/ucsc-mrnatogene

recipes/ucsc-netchainsubset

recipes/ucsc-netclass

recipes/ucsc-netfilter

recipes/ucsc-netsplit

recipes/ucsc-netsyntenic

recipes/ucsc-nettoaxt

recipes/ucsc-nettobed

recipes/ucsc-newprog

recipes/ucsc-newpythonprog

recipes/ucsc-nibfrag

recipes/ucsc-nibsize

recipes/ucsc-oligomatch

recipes/ucsc-overlapselect

recipes/ucsc-para

recipes/ucsc-parafetch

recipes/ucsc-parahub

recipes/ucsc-parahubstop

recipes/ucsc-paranode

recipes/ucsc-paranodestart

recipes/ucsc-paranodestatus

recipes/ucsc-paranodestop

recipes/ucsc-parasol

recipes/ucsc-parasync

recipes/ucsc-paratestjob

recipes/ucsc-positionaltblcheck

recipes/ucsc-pslcat

recipes/ucsc-pslcheck

recipes/ucsc-psldropoverlap

recipes/ucsc-pslfilter

recipes/ucsc-pslhisto

recipes/ucsc-pslliftsubrangeblat

recipes/ucsc-pslmap

recipes/ucsc-pslmappostchain

recipes/ucsc-pslmrnacover

recipes/ucsc-pslpairs

recipes/ucsc-pslpartition

recipes/ucsc-pslpostarget

recipes/ucsc-pslpretty

recipes/ucsc-pslrc

recipes/ucsc-pslrecalcmatch

recipes/ucsc-pslreps

recipes/ucsc-pslscore

recipes/ucsc-pslselect

recipes/ucsc-pslsomerecords

recipes/ucsc-pslsort

recipes/ucsc-pslstats

recipes/ucsc-pslswap

recipes/ucsc-psltobed

recipes/ucsc-psltobigpsl

recipes/ucsc-psltochain

recipes/ucsc-psltopslx

recipes/ucsc-pslxtofa

recipes/ucsc-qacagplift

recipes/ucsc-qactoqa

recipes/ucsc-qactowig

recipes/ucsc-qatoqac

recipes/ucsc-randomlines

recipes/ucsc-rasqlquery

recipes/ucsc-ratolines

recipes/ucsc-ratotab

recipes/ucsc-rmfadups

recipes/ucsc-rowstocols

recipes/ucsc-spacedtotab

recipes/ucsc-splitfile

recipes/ucsc-splitfilebycolumn

recipes/ucsc-sqltoxml

recipes/ucsc-stringify

recipes/ucsc-subchar

recipes/ucsc-subcolumn

recipes/ucsc-taillines

recipes/ucsc-tdbquery

recipes/ucsc-texthistogram

recipes/ucsc-ticktodate

recipes/ucsc-tolower

recipes/ucsc-toupper

recipes/ucsc-transmappsltogenepred

recipes/ucsc-trfbig

recipes/ucsc-twobitdup

recipes/ucsc-twobitmask

recipes/ucsc-validatefiles

recipes/ucsc-validatemanifest

recipes/ucsc-websync

recipes/ucsc-wigcorrelate

recipes/ucsc-wordline

recipes/ucsc-xmlcat

recipes/ucsc-xmltosql

# Above v1.0.5 there are licensing restrictions and it cannot be distributed

# via bioconda. See https://github.com/bioconda/bioconda-recipes/pull/23476.

recipes/fishtaco

# version 0.3 referred to in recipe is no longer available, latest is 0.2-beta

recipes/rnacode

# source is no longer available

recipes/sweepfinder2

# syntax error in configure script

recipes/kat

# permission error

recipes/perl-gd

# sha mismatch when downloading source

recipes/fmlrc2

# tries to download zlib itself, which fails

recipes/d4binding