Re: [galaxy-dev] Infinite recursion on conda dependency manager
Hi Björn, this is not working root@galaxy:/galaxy-central# export PATH=/galaxy-central/tool_deps/_conda/bin/:$PATH root@galaxy:/galaxy-central# conda install -y -q conda=3.19.3 bash: conda: command not found cheers, Philipp -Original message- From: Björn Grüning Sent: Monday 20th June 2016 13:21 To: Rathert, Philipp, Dr. ; galaxy-dev@lists.galaxyproject.org Cc: Björn Grüning Subject: Re: [galaxy-dev] Infinite recursion on conda dependency manager Hi Philipp, you are inside of the Docker container? Can you do a: export PATH=/galaxy-central/tool_deps/_conda/bin/:$PATH conda install -y -q conda=3.19.3 Ciao, Bjoern Am 20.06.2016 um 13:01 schrieb Rathert, Philipp, Dr.: > Dear all, > > > > > > I am trying to install bowtie as a dependency for bismarck. however, I am > getting the error posted below. > > > > Maybe somebody has an idea how to fix this. > > > > > > Thanks in advance, > > > > philipp > > > > > > In file included from SeqAn-1.1/seqan/basic.h:64:0, > from SeqAn-1.1/seqan/sequence.h:27, > from SeqAn-1.1/seqan/index.h:27, > from ebwt_build.cpp:5: > SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void > seqan::setValue(seqan::Holder&, TValue&)’: > SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef ‘THolderType’ > locally defined but not used [-Wunused-local-typedefs] > typedef typename Value >::Type THolderType; >ˆ > SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘typename > seqan::Reference >::Type > seqan::value(seqan::Holder&)’: > SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef ‘THolderType’ > locally defined but not used [-Wunused-local-typedefs] > typedef typename Value >::Type THolderType; >ˆ > SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void > seqan::assignValue(seqan::Holder&, const TSource&)’: > SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef ‘THostValue’ > locally defined but not used [-Wunused-local-typedefs] > typedef typename Value >::Type THostValue; >ˆ > In file included from SeqAn-1.1/seqan/sequence.h:38:0, > from SeqAn-1.1/seqan/index.h:27, > from ebwt_build.cpp:5: > SeqAn-1.1/seqan/sequence/lexical.h: In function ‘void > seqan::compare_(seqan::Lexical&, TLeft&, TRight&)’: > SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef ‘TLeftValue’ > locally defined but not used [-Wunused-local-typedefs] > typedef typename Value::Type TLeftValue; > ˆ > In file included from SeqAn-1.1/seqan/sequence.h:51:0, > from SeqAn-1.1/seqan/index.h:27, > from ebwt_build.cpp:5: > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void > seqan::assign(seqan::String&, const TSource&, > seqan::Tag)’: > SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef ‘TTarget’ > locally defined but not used [-Wunused-local-typedefs] > typedef String TTarget; > ˆ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void > seqan::assign(seqan::String&, const TSource&, TSize, > seqan::Tag)’: > SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef ‘TTarget’ > locally defined but not used [-Wunused-local-typedefs] > typedef String TTarget; > ˆ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void > seqan::assign(seqan::String&, const TSourceValue*, > seqan::Tag)’: > SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef ‘TTarget’ > locally defined but not used [-Wunused-local-typedefs] > typedef String TTarget; > ˆ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void > seqan::assign(seqan::String&, const TSourceValue*, TSize, > seqan::Tag)’: > SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef ‘TTarget’ > locally defined but not used [-Wunused-local-typedefs] > typedef String TTarget; > ˆ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void > seqan::append(seqan::String&, const TSource&, > seqan::Tag)’: > SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef ‘TTarget’ > locally defined but not used [-Wunused-local-typedefs] > typedef String TTarget; > ˆ > SeqAn-1.1/seqan/seque
Re: [galaxy-dev] Infinite recursion on conda dependency manager
onst TSource&, > seqan::Tag)’: > SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef ‘TTarget’ > locally defined but not used [-Wunused-local-typedefs] > typedef String TTarget; > ^ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void > seqan::append(seqan::String&, const TSource&, typename > seqan::Size >::Type, seqan::Tag)’: > SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef ‘TTarget’ > locally defined but not used [-Wunused-local-typedefs] > typedef String TTarget; > ^ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void > seqan::append(seqan::String&, TSourceValue*, > seqan::Tag)’: > SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef ‘TTarget’ > locally defined but not used [-Wunused-local-typedefs] > typedef String TTarget; > ^ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void > seqan::append(seqan::String&, TSourceValue*, typename > seqan::Size >::Type, seqan::Tag)’: > SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef ‘TTarget’ > locally defined but not used [-Wunused-local-typedefs] > typedef String TTarget; > ^ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void > seqan::replace(seqan::String&, typename > seqan::Size >::Type, typename > seqan::Size >::Type, const TSource&, > seqan::Tag)’: > SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef ‘TTarget’ > locally defined but not used [-Wunused-local-typedefs] > typedef String TTarget; > ^ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void > seqan::replace(seqan::String&, typename > seqan::Size >::Type, typename > seqan::Size >::Type, const TSource&, typename > seqan::Size >::Type, seqan::Tag)’: > SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef ‘TTarget’ > locally defined but not used [-Wunused-local-typedefs] > typedef String TTarget; > ^ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void > seqan::replace(seqan::String&, typename > seqan::Size >::Type, typename > seqan::Size >::Type, const TSourceValue*, > seqan::Tag)’: > SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef ‘TTarget’ > locally defined but not used [-Wunused-local-typedefs] > typedef String TTarget; > ^ > SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void > seqan::replace(seqan::String&, typename > seqan::Size >::Type, typename > seqan::Size >::Type, const TSourceValue*, > typename seqan::Size >::Type, > seqan::Tag)’: > SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef ‘TTarget’ > locally defined but not used [-Wunused-local-typedefs] > typedef String TTarget; > ^ > In file included from SeqAn-1.1/seqan/sequence.h:53:0, > from hit.h:11, > from hit.cpp:1: > SeqAn-1.1/seqan/sequence/string_alloc.h: In function ‘typename > seqan::Size > >::Type > seqan::reserve(seqan::String >&, _TSize, Insist)’: > SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef ‘TSize’ > locally defined but not used [-Wunused-local-typedefs] > typedef typename Size< String > >::Type TSize; >^ > In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from hit.h:11, > from hit.cpp:1: > SeqAn-1.1/seqan/sequence/string_packed.h: In static member function ‘static > typename seqan::Size::Type > seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename > seqan::Size::Type, typename seqan::Size::Type, typename > seqan::Size::Type, typename seqan::Size::Type)’: > SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef ‘TIterator’ > locally defined but not used [-Wunused-local-typedefs] >typedef typename Iterator::Type TIterator; > ^ > SeqAn-1.1/seqan/sequence/string_packed.h: In function ‘typename > seqan::Size > >::Type > seqan::reserve(seqan::String >&, _TSize, > Insist)’: > SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef ‘TSize’ > locally defined but not used [-Wunused-local-typedefs] > typedef typename Size< String > >::Type TSize; >^ > In file includ
Re: [galaxy-dev] Infinite recursion on conda dependency manager
Hi Peter, please install conda in version 3.19.3. Conda-4 has a bug when using with --offline and --local. conda install conda=3.19.3 should work. https://github.com/galaxyproject/tools-iuc/blob/master/.travis.yml#L15 Thanks, Bjoern Am 15.06.2016 um 00:44 schrieb Peter van Heusden: > Hi there > > I've got a package in our lab conda channel (its still in testing phase) > called goget. This is specified as a requirement for the build_ctb_gene > tool like this: > > >goget > > > When the tool runs, I see infinite recursion on the conda side: > > https://gist.github.com/pvanheus/c16a07a2c954741a311881cc7606df8d > > Any ideas? > > Thanks, > Peter > > > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Infinite recursion on conda dependency manager
Hi there I've got a package in our lab conda channel (its still in testing phase) called goget. This is specified as a requirement for the build_ctb_gene tool like this: goget When the tool runs, I see infinite recursion on the conda side: https://gist.github.com/pvanheus/c16a07a2c954741a311881cc7606df8d Any ideas? Thanks, Peter ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/