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 <bjoern.gruen...@gmail.com>
Sent: Monday 20th June 2016 13:21
To: Rathert, Philipp, Dr. <philipp.rath...@ibc.uni-stuttgart.de>; 
galaxy-dev@lists.galaxyproject.org
Cc: Björn Grüning <bjoern.gruen...@gmail.com>
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::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THolderType;
>                                                            ˆ
> SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘typename 
> seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type 
> seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)’:
> SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef ‘THolderType’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                            ˆ
> SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void 
> seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::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<TSpec>&, 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<TLeft>::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<TValue, TSpec>&, const TSource&, 
> seqan::Tag<TUsage>)’:
> SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
>                                             ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, 
> seqan::Tag<TUsage>)’:
> SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
>                                             ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, 
> seqan::Tag<TUsage>)’:
> SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
>                                             ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, 
> seqan::Tag<TUsage>)’:
> SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
>                                             ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::append(seqan::String<TValue, TSpec>&, const TSource&, 
> seqan::Tag<TUsage>)’:
> SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
>                                             ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename 
> seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
> SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
>                                             ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, 
> seqan::Tag<TUsage>)’:
> SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
>                                             ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename 
> seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
> SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
>                                             ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::replace(seqan::String<TValue, TSpec>&, typename 
> seqan::Size<seqan::String<TValue, TSpec> >::Type, typename 
> seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, 
> seqan::Tag<TUsage>)’:
> SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
>                                             ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::replace(seqan::String<TValue, TSpec>&, typename 
> seqan::Size<seqan::String<TValue, TSpec> >::Type, typename 
> seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename 
> seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
> SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
>                                             ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::replace(seqan::String<TValue, TSpec>&, typename 
> seqan::Size<seqan::String<TValue, TSpec> >::Type, typename 
> seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, 
> seqan::Tag<TUsage>)’:
> SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
>                                             ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::replace(seqan::String<TValue, TSpec>&, typename 
> seqan::Size<seqan::String<TValue, TSpec> >::Type, typename 
> seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, 
> typename seqan::Size<seqan::String<TValue, TSpec> >::Type, 
> seqan::Tag<TUsage>)’:
> SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
>                                             ˆ
> In file included from SeqAn-1.1/seqan/sequence.h:53:0,
>                  from SeqAn-1.1/seqan/index.h:27,
>                  from ebwt_build.cpp:5:
> SeqAn-1.1/seqan/sequence/string_alloc.h: In function ‘typename 
> seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type 
> seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize;
>                                                                ˆ
> In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                  from SeqAn-1.1/seqan/index.h:27,
>                  from ebwt_build.cpp:5:
> SeqAn-1.1/seqan/sequence/string_packed.h: In static member function ‘static 
> typename seqan::Size<T>::Type 
> seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename 
> seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename 
> seqan::Size<T>::Type, typename seqan::Size<T>::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<T, Standard>::Type TIterator;
>                                                 ˆ
> SeqAn-1.1/seqan/sequence/string_packed.h: In function ‘typename 
> seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type 
> seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize;
>                                                                ˆ
> In file included from SeqAn-1.1/seqan/sequence.h:62:0,
>                  from SeqAn-1.1/seqan/index.h:27,
>                  from ebwt_build.cpp:5:
> SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function ‘void 
> seqan::subset(seqan::StringSet<TString, seqan::Dependent<const 
> seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, 
> seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)’:
> SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef ‘TId’ 
> locally defined but not used [-Wunused-local-typedefs]
>    typedef typename Id<TStringSet>::Type TId;
>                                          ˆ
> In file included from SeqAn-1.1/seqan/index.h:82:0,
>                  from ebwt_build.cpp:5:
> SeqAn-1.1/seqan/index/shape_base.h: In function ‘typename 
> seqan::Value<seqan::Shape<TValue, seqan::FixedShape<0u> > >::Type 
> seqan::hash(seqan::Shape<TValue, seqan::FixedShape<0u> >&, TIter)’:
> SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef ‘THValue’ locally 
> defined but not used [-Wunused-local-typedefs]
>    typedef typename Value< Shape<TValue, SimpleShape> >::Type THValue;
>                                                               ˆ
> SeqAn-1.1/seqan/index/shape_base.h: In function ‘typename 
> seqan::Value<seqan::Shape<TValue, seqan::FixedShape<q> > >::Type 
> seqan::hash(seqan::Shape<TValue, seqan::FixedShape<q> >&, TIter)’:
> SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef ‘THValue’ locally 
> defined but not used [-Wunused-local-typedefs]
>    typedef typename Value< Shape<TValue, FixedShape<q> > >::Type THValue;
>                                                                  ˆ
> SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef ‘TSize’ locally 
> defined but not used [-Wunused-local-typedefs]
>    typedef typename Size< Shape<TValue, FixedShape<q> > >::Type TSize;
>                                                                 ˆ
> SeqAn-1.1/seqan/index/shape_base.h: In function ‘typename 
> seqan::Value<seqan::Shape<TValue, TSpec> >::Type 
> seqan::hash(seqan::Shape<TValue, TSpec>&, TIter, TSize)’:
> SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef ‘THValue’ locally 
> defined but not used [-Wunused-local-typedefs]
>    typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
>                                                         ˆ
> SeqAn-1.1/seqan/index/shape_base.h: In function ‘typename 
> seqan::Value<seqan::Shape<TValue, TSpec> >::Type 
> seqan::hashUpper(seqan::Shape<TValue, TSpec>&, TIter, TSize)’:
> SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef ‘THValue’ locally 
> defined but not used [-Wunused-local-typedefs]
>    typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
>                                                         ˆ
> SeqAn-1.1/seqan/index/shape_base.h: In function ‘typename 
> seqan::Value<seqan::Shape<TValue, TSpec> >::Type 
> seqan::hash2(seqan::Shape<TValue, TSpec>&, TIter, TSize)’:
> SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef ‘THValue’ locally 
> defined but not used [-Wunused-local-typedefs]
>    typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
>                                                         ˆ
> In file included from SeqAn-1.1/seqan/index.h:83:0,
>                  from ebwt_build.cpp:5:
> SeqAn-1.1/seqan/index/shape_gapped.h: In function ‘typename 
> seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<const 
> seqan::Tag<seqan::Default_> > > >::Type seqan::hash(seqan::Shape<TValue, 
> seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > >&, TIter)’:
> SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef ‘THValue’ 
> locally defined but not used [-Wunused-local-typedefs]
>    typedef typename Value< Shape<TValue, GappedShape> >::Type THValue;
>                                                               ˆ
> SeqAn-1.1/seqan/index/shape_gapped.h: In function ‘typename 
> seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type 
> seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, 
> TSize)’:
> SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef ‘THValue’ 
> locally defined but not used [-Wunused-local-typedefs]
>    typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type 
> THValue;
>                                                                            ˆ
> SeqAn-1.1/seqan/index/shape_gapped.h: In function ‘typename 
> seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type 
> seqan::hashUpper(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, 
> TIter, TSize)’:
> SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef ‘THValue’ 
> locally defined but not used [-Wunused-local-typedefs]
>    typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type 
> THValue;
>                                                                            ˆ
> In file included from SeqAn-1.1/seqan/file.h:66:0,
>                  from ebwt_build.cpp:7:
> SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void 
> seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)’:
> SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 
> ‘TRow’ locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Row<TAlign>::Type TRow;
>                                      ˆ
> SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void 
> seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, 
> FastaAlign)’:
> SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 
> ‘TPosition’ locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Position<TAlign>::Type TPosition;
>                                           ˆ
> In file included from SeqAn-1.1/seqan/file.h:69:0,
>                  from ebwt_build.cpp:7:
> SeqAn-1.1/seqan/file/file_format_cgviz.h: In function ‘void 
> seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, 
> CGViz)’:
> SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef ‘TRow’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Row<TAlign>::Type TRow;
>                                      ˆ
> In file included from ebwt.h:27:0,
>                  from ebwt_build.cpp:11:
> blockwise_sa.h: In member function ‘void 
> KarkkainenBlockwiseSA<TStr>::buildSamples()’:
> blockwise_sa.h:380:37: warning: typedef ‘TAlphabet’ locally defined but not 
> used [-Wunused-local-typedefs]
>   typedef typename Value<TStr>::Type TAlphabet;
>                                      ˆ
> blockwise_sa.h: In member function ‘virtual void 
> KarkkainenBlockwiseSA<TStr>::nextBlock()’:
> blockwise_sa.h:745:37: warning: typedef ‘TAlphabet’ locally defined but not 
> used [-Wunused-local-typedefs]
>   typedef typename Value<TStr>::Type TAlphabet;
>                                      ˆ
> In file included from ebwt.h:1607:0,
>                  from ebwt_build.cpp:11:
> ebwt_search_backtrack.h: In member function ‘bool 
> GreedyDFSRangeSource::backtrack(uint32_t, uint32_t, uint32_t, uint32_t, 
> uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t*, 
> uint8_t*, bool)’:
> ebwt_search_backtrack.h:772:11: warning: variable ‘foundTarget’ set but not 
> used [-Wunused-but-set-variable]
>     
> ..
> TTarget’ locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
>                                             ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::replace(seqan::String<TValue, TSpec>&, typename 
> seqan::Size<seqan::String<TValue, TSpec> >::Type, typename 
> seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, 
> seqan::Tag<TUsage>)’:
> SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
>                                             ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::replace(seqan::String<TValue, TSpec>&, typename 
> seqan::Size<seqan::String<TValue, TSpec> >::Type, typename 
> seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, 
> typename seqan::Size<seqan::String<TValue, TSpec> >::Type, 
> seqan::Tag<TUsage>)’:
> SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
>                                             ˆ
> In file included from SeqAn-1.1/seqan/sequence.h:53:0,
>                  from alphabet.h:6,
>                  from color_dec.cpp:11:
> SeqAn-1.1/seqan/sequence/string_alloc.h: In function ‘typename 
> seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type 
> seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize;
>                                                                ˆ
> In file included from SeqAn-1.1/seqan/sequence.h:57:0,
>                  from alphabet.h:6,
>                  from color_dec.cpp:11:
> SeqAn-1.1/seqan/sequence/string_packed.h: In static member function ‘static 
> typename seqan::Size<T>::Type 
> seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename 
> seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename 
> seqan::Size<T>::Type, typename seqan::Size<T>::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<T, Standard>::Type TIterator;
>                                                 ˆ
> SeqAn-1.1/seqan/sequence/string_packed.h: In function ‘typename 
> seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type 
> seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize;
>                                                                ˆ
> In file included from SeqAn-1.1/seqan/sequence.h:62:0,
>                  from alphabet.h:6,
>                  from color_dec.cpp:11:
> SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function ‘void 
> seqan::subset(seqan::StringSet<TString, seqan::Dependent<const 
> seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, 
> seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)’:
> SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef ‘TId’ 
> locally defined but not used [-Wunused-local-typedefs]
>    typedef typename Id<TStringSet>::Type TId;
>                                          ˆ
> In file included from SeqAn-1.1/seqan/file.h:66:0,
>                  from alphabet.h:7,
>                  from color_dec.cpp:11:
> SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void 
> seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)’:
> SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 
> ‘TRow’ locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Row<TAlign>::Type TRow;
>                                      ˆ
> SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void 
> seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, 
> FastaAlign)’:
> SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 
> ‘TPosition’ locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Position<TAlign>::Type TPosition;
>                                           ˆ
> In file included from SeqAn-1.1/seqan/file.h:69:0,
>                  from alphabet.h:7,
>                  from color_dec.cpp:11:
> SeqAn-1.1/seqan/file/file_format_cgviz.h: In function ‘void 
> seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, 
> CGViz)’:
> SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef ‘TRow’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Row<TAlign>::Type TRow;
>                                      ˆ
> color_dec.cpp: In function ‘void decodeHit(const char*, const char*, size_t, 
> size_t, const char*, size_t, size_t, int, char*, char*, char*, int&, int&)’:
> color_dec.cpp:187:6: warning: variable ‘lastOmin’ set but not used 
> [-Wunused-but-set-variable]
>   int lastOmin = INT_MAX;
>       ˆ
> In file included from SeqAn-1.1/seqan/basic.h:64:0,
>                  from SeqAn-1.1/seqan/sequence.h:27,
>                  from hit.h:11,
>                  from hit.cpp:1:
> SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void 
> seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THolderType;
>                                                            ˆ
> SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘typename 
> seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type 
> seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)’:
> SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef ‘THolderType’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
>                                                            ˆ
> SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void 
> seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THostValue;
>                                                            ˆ
> In file included from SeqAn-1.1/seqan/sequence.h:38:0,
>                  from hit.h:11,
>                  from hit.cpp:1:
> SeqAn-1.1/seqan/sequence/lexical.h: In function ‘void 
> seqan::compare_(seqan::Lexical<TSpec>&, 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<TLeft>::Type TLeftValue;
>                                       ˆ
> In file included from SeqAn-1.1/seqan/sequence.h:51:0,
>                  from hit.h:11,
>                  from hit.cpp:1:
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, 
> seqan::Tag<TUsage>)’:
> SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
>                                             ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, 
> seqan::Tag<TUsage>)’:
> SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
>                                             ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, 
> seqan::Tag<TUsage>)’:
> SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
>                                             ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, 
> seqan::Tag<TUsage>)’:
> SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
>                                             ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::append(seqan::String<TValue, TSpec>&, const TSource&, 
> seqan::Tag<TUsage>)’:
> SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
>                                             ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename 
> seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
> SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
>                                             ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, 
> seqan::Tag<TUsage>)’:
> SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
>                                             ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename 
> seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
> SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
>                                             ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::replace(seqan::String<TValue, TSpec>&, typename 
> seqan::Size<seqan::String<TValue, TSpec> >::Type, typename 
> seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, 
> seqan::Tag<TUsage>)’:
> SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
>                                             ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::replace(seqan::String<TValue, TSpec>&, typename 
> seqan::Size<seqan::String<TValue, TSpec> >::Type, typename 
> seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename 
> seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
> SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
>                                             ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::replace(seqan::String<TValue, TSpec>&, typename 
> seqan::Size<seqan::String<TValue, TSpec> >::Type, typename 
> seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, 
> seqan::Tag<TUsage>)’:
> SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
>                                             ˆ
> SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void 
> seqan::replace(seqan::String<TValue, TSpec>&, typename 
> seqan::Size<seqan::String<TValue, TSpec> >::Type, typename 
> seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, 
> typename seqan::Size<seqan::String<TValue, TSpec> >::Type, 
> seqan::Tag<TUsage>)’:
> SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef ‘TTarget’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef String<TTargetValue, TTargetSpec> TTarget;
>                                             ˆ
> 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<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type 
> seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize;
>                                                                ˆ
> 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<T>::Type 
> seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename 
> seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename 
> seqan::Size<T>::Type, typename seqan::Size<T>::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<T, Standard>::Type TIterator;
>                                                 ˆ
> SeqAn-1.1/seqan/sequence/string_packed.h: In function ‘typename 
> seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type 
> seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize;
>                                                                ˆ
> In file included from SeqAn-1.1/seqan/sequence.h:62:0,
>                  from hit.h:11,
>                  from hit.cpp:1:
> SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function ‘void 
> seqan::subset(seqan::StringSet<TString, seqan::Dependent<const 
> seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, 
> seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)’:
> SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef ‘TId’ 
> locally defined but not used [-Wunused-local-typedefs]
>    typedef typename Id<TStringSet>::Type TId;
>                                          ˆ
> In file included from SeqAn-1.1/seqan/file.h:66:0,
>                  from alphabet.h:7,
>                  from hit.h:12,
>                  from hit.cpp:1:
> SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void 
> seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)’:
> SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 
> ‘TRow’ locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Row<TAlign>::Type TRow;
>                                      ˆ
> SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void 
> seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, 
> FastaAlign)’:
> SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 
> ‘TPosition’ locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Position<TAlign>::Type TPosition;
>                                           ˆ
> In file included from SeqAn-1.1/seqan/file.h:69:0,
>                  from alphabet.h:7,
>                  from hit.h:12,
>                  from hit.cpp:1:
> SeqAn-1.1/seqan/file/file_format_cgviz.h: In function ‘void 
> seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, 
> CGViz)’:
> SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef ‘TRow’ 
> locally defined but not used [-Wunused-local-typedefs]
>   typedef typename Row<TAlign>::Type TRow;
>                                      ˆ
> make: *** [bowtie] Error 1
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> -----Original message-----
> From: Björn Grüning <bjoern.gruen...@gmail.com>
> Sent: Wednesday 15th June 2016 9:09
> To: Peter van Heusden <p...@sanbi.ac.za>; galaxy-dev@lists.galaxyproject.org
> Subject: 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:
>>
>>     <requirements>
>>        <requirement type="package" version="0.0.1">goget</requirement>
>>     </requirements>
>>
>> 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/
>>
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>>   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:
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> 
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> 


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