galaxy-dev June 2016

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Re: [galaxy-dev] Infinite recursion on conda dependency manager
by Rathert, Philipp, Dr. 20 Jun '16

20 Jun '16

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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ 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; ^ make: *** [bowtie] Error 1 -----Original message----- From: Björn Grüning <bjoern.gruening(a)gmail.com> Sent: Wednesday 15th June 2016 9:09 To: Peter van Heusden <pvh(a)sanbi.ac.za>; galaxy-dev(a)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/ > > 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/

2 1

Re: [galaxy-dev] History is not up-to-date
by Rathert, Philipp, Dr. 20 Jun '16

20 Jun '16

Hi Carl, it looks like the time is not correct. System Time: 2016-06-20T09:30:00.038328386Z EventsListeners: 0 Init SHA1: Init Path: /usr/local/bin/docker Docker Root Dir: /mnt/sda1/var/lib/docker Labels: provider=virtualbox the clock on my mac says 11:25 Is there an easy way to fix this or do I need to run galaxy in a new container? I run the container with -privileged=true, so it should be possible but so far I didn't find how... Thanks for your help. Cheers, Philipp -----Original message----- From: Philipp Rathert <philipp.rathert(a)ibc.uni-stuttgart.de> Sent: Wednesday 15th June 2016 9:07 To: 'Carl Eberhard' <carlfeberhard(a)gmail.com> Cc: galaxy-dev(a)lists.galaxyproject.org Subject: Re: [galaxy-dev] History is not up-to-date HI Carl, I am travelling these days but will check on Monday. Thanks in advance. Cheers, Philipp From: Carl Eberhard [mailto:carlfeberhard@gmail.com] Sent: Tuesday, June 14, 2016 6:24 PM To: Rathert, Philipp, Dr. <philipp.rathert(a)ibc.uni-stuttgart.de> Cc: galaxy-dev(a)lists.galaxyproject.org Subject: Re: [galaxy-dev] History is not up-to-date Hi, Phillip Quick questions: - is the time properly set on the computer where you've got Galaxy running in the browser? - is the time in the docker container also correct? From you terminal output it looks like the update time might be the issue and we can then take it from there. Thanks On Tue, Jun 14, 2016 at 11:28 AM, Rathert, Philipp, Dr. <philipp.rathert(a)ibc.uni-stuttgart.de <mailto:philipp.rathert@ibc.uni-stuttgart.de> > wrote: Dear All, I have a problem with my histories. We are running the Docker galaxy stable version 16.04 and when I start a tool the history does not show that it is running. it is not specific for any tool but for all. however, something is running in the back 129.69.102.30 - - [14/Jun/2016:12:57:21 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A16.601Z HTTP/1.1" 200 - "http://129.69.102.42/ <http://129.69.102.42/> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 271|app: 0|req: 74/163] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:21 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A16.601Z => generated 2511 bytes in 33 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 2) 129.69.102.30 - - [14/Jun/2016:12:57:25 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A20.635Z HTTP/1.1" 200 - "http://129.69.102.42/ <http://129.69.102.42/> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 271|app: 0|req: 75/164] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:25 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A20.635Z => generated 2511 bytes in 29 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 1) 129.69.102.30 - - [14/Jun/2016:12:57:29 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A24.673Z HTTP/1.1" 200 - "http://129.69.102.42/ <http://129.69.102.42/> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 271|app: 0|req: 76/165] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:29 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A24.673Z => generated 2112 bytes in 30 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 0) 129.69.102.30 - - [14/Jun/2016:12:57:33 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A28.711Z HTTP/1.1" 200 - "http://129.69.102.42/ <http://129.69.102.42/> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 272|app: 0|req: 90/166] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:33 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A28.711Z => generated 2112 bytes in 32 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 0) 129.69.102.30 - - [14/Jun/2016:12:57:37 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A32.749Z HTTP/1.1" 200 - "http://129.69.102.42/ <http://129.69.102.42/> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 271|app: 0|req: 77/167] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:37 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A32.749Z => generated 2112 bytes in 27 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 3) I am not sure how to fix this and I am happy for any suggestion. Cheers, Philipp ___________________________________________________________ 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/ <http://galaxyproject.org/search/mailinglists/>

3 2

Re: [galaxy-dev] History is not up-to-date
by Rathert, Philipp, Dr. 20 Jun '16

20 Jun '16

Dear Nicola, I am using the 16.04 release. did you implement changes in this one recently? Cheers, Philipp -----Original message----- From: Nicola Soranzo <nsoranzo(a)tiscali.it> Sent: Monday 20th June 2016 12:16 To: Rathert, Philipp, Dr. <philipp.rathert(a)ibc.uni-stuttgart.de>; 'Carl Eberhard' <carlfeberhard(a)gmail.com> Cc: galaxy-dev(a)lists.galaxyproject.org Subject: Re: [galaxy-dev] History is not up-to-date Hi Philipp, this has been fixed in the mean time on the release_16.04 branch of Galaxy, see https://github.com/galaxyproject/galaxy/pull/2506 Can you try to update your Galaxy server in the container and check if it's working? Cheers, Nicola On 20/06/16 10:31, Rathert, Philipp, Dr. wrote: Hi Carl, it looks like the time is not correct. System Time: 2016-06-20T09:30:00.038328386Z EventsListeners: 0 Init SHA1: Init Path: /usr/local/bin/docker Docker Root Dir: /mnt/sda1/var/lib/docker Labels: provider=virtualbox the clock on my mac says 11:25 Is there an easy way to fix this or do I need to run galaxy in a new container? I run the container with -privileged=true, so it should be possible but so far I didn't find how... Thanks for your help. Cheers, Philipp -----Original message----- From: Philipp Rathert <philipp.rathert(a)ibc.uni-stuttgart.de> Sent: Wednesday 15th June 2016 9:07 To: 'Carl Eberhard' <carlfeberhard(a)gmail.com> Cc: galaxy-dev(a)lists.galaxyproject.org Subject: Re: [galaxy-dev] History is not up-to-date HI Carl, I am travelling these days but will check on Monday. Thanks in advance. Cheers, Philipp From: Carl Eberhard [mailto:carlfeberhard@gmail.com] Sent: Tuesday, June 14, 2016 6:24 PM To: Rathert, Philipp, Dr. <philipp.rathert(a)ibc.uni-stuttgart.de> Cc: galaxy-dev(a)lists.galaxyproject.org Subject: Re: [galaxy-dev] History is not up-to-date Hi, Phillip Quick questions: - is the time properly set on the computer where you've got Galaxy running in the browser? - is the time in the docker container also correct? From you terminal output it looks like the update time might be the issue and we can then take it from there. Thanks On Tue, Jun 14, 2016 at 11:28 AM, Rathert, Philipp, Dr. <philipp.rathert(a)ibc.uni-stuttgart.de> wrote: Dear All, I have a problem with my histories. We are running the Docker galaxy stable version 16.04 and when I start a tool the history does not show that it is running. it is not specific for any tool but for all. however, something is running in the back 129.69.102.30 - - [14/Jun/2016:12:57:21 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A16.601Z HTTP/1.1" 200 - "http://129.69.102.42/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 271|app: 0|req: 74/163] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:21 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A16.601Z => generated 2511 bytes in 33 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 2) 129.69.102.30 - - [14/Jun/2016:12:57:25 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A20.635Z HTTP/1.1" 200 - "http://129.69.102.42/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 271|app: 0|req: 75/164] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:25 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A20.635Z => generated 2511 bytes in 29 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 1) 129.69.102.30 - - [14/Jun/2016:12:57:29 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A24.673Z HTTP/1.1" 200 - "http://129.69.102.42/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 271|app: 0|req: 76/165] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:29 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A24.673Z => generated 2112 bytes in 30 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 0) 129.69.102.30 - - [14/Jun/2016:12:57:33 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A28.711Z HTTP/1.1" 200 - "http://129.69.102.42/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 272|app: 0|req: 90/166] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:33 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A28.711Z => generated 2112 bytes in 32 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 0) 129.69.102.30 - - [14/Jun/2016:12:57:37 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A32.749Z HTTP/1.1" 200 - "http://129.69.102.42/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 271|app: 0|req: 77/167] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:37 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A32.749Z => generated 2112 bytes in 27 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 3) I am not sure how to fix this and I am happy for any suggestion. Cheers, Philipp ___________________________________________________________ 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/

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Building Galaxy Tool: cannot find 'is_of_type'
by Nikolaos Tur 19 Jun '16

19 Jun '16

Hi, according to https://planemo.readthedocs.io/en/latest/writing_how_do_i.html#check-input-… and https://bitbucket.org/galaxy/galaxy-central/pull-requests/457/allow-cheetah… there is simple function for data type checking: is_of_type() after running job is not prepared and fail with: galaxy.jobs.runners ERROR 2016-06-19 18:46:16,257 (66) Failure preparing job Traceback (most recent call last): File "/home/galaxy/lib/galaxy/jobs/runners/__init__.py", line 169, in prepare_job job_wrapper.prepare() File "/home/galaxy/lib/galaxy/jobs/__init__.py", line 889, in prepare self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build() File "/home/galaxy/lib/galaxy/tools/evaluation.py", line 445, in build raise e NotFound: cannot find 'is_of_type' while searching for 'is_of_type' where part of wrapper with is_of_type() is: <command> <![CDATA[ #if $reads.is_of_type('fastq'): ln -s "$reads" rInput1.fq && #set $reads = 'rInput1.fq' #end if ... where am I wrong? Or that is a Galaxy bug? Galxy is 16.04 and is_of_type() function is defined in lib/galaxy/tools/wrappers.py Thanx, Nikolaos

1 0

flexbar v2.7 & required format extension
by Nikolaos Tur 19 Jun '16

19 Jun '16

Hi, does someone use latest version of flexbar 2.7 with Galaxy? It seems newest flexbar changes way how it works with data. Now it requires format extension for data. But Galaxy operates data with .dat extension in database/files/. Also there is flexbar wrapper for version 2.7, so it should be somehow integrated to the Galaxy. Our Galaxy is 16.04. Thanx, Nikolaos

2 3

GalaxyAdmins Meetup This Thursday
by Dave Clements 16 Jun '16

16 Jun '16

Hello all, The June online meetup of GalaxyAdmins will be this Thursday <https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2016_06_16>. This month features two talks: *1. Galaxy in Production at the University of Minnesota* [image: Minnesota Supercomputing Institute] <https://www.msi.umn.edu/> [image: Galaxy Radio Telescope] <https://github.com/galaxyproject/galaxy/pull/2455> Galaxy has been deployed in several contexts by the Minnesota Supercomputing Institute (MSI) <https://www.msi.umn.edu/> at the University of Minnesota - Twin Citites <https://www.umn.edu/>. This month Evan Bollig <https://www.msi.umn.edu/staff/evan> and JJ Johnson <https://www.msi.umn.edu/staff/jj> of MSI will discuss several aspects of this work relevant to the GalaxyAdmins <https://wiki.galaxyproject.org/GalaxyAdmins> group: - customizations made to Galaxy that enable MSI to leverage it as a Tier I service <https://www.msi.umn.edu/services> for our users (e.g., scheduling, quotas, billing, and sharing). - Pulsar <https://github.com/galaxyproject/pulsar> for Galaxy-P <https://usegalaxyp.org/> tools on Windows. - the CLIA-certified <http://www.fda.gov/MedicalDevices/DeviceRegulationandGuidance/IVDRegulatory…> pipelines and how Galaxy is integrated into clinical workflows *2. Galaxy Radio Telescope* The GRT <https://github.com/galaxyproject/galaxy/pull/2455> aims to collect job run information from Galaxy servers that opt into the process. Galaxy Admins can sign in to the GRT, register their Galaxy servers, and get back API keys per-Galaxy instance. Then they set up a cron job (preferably weekly, but we may explore options here later), and submit job data to the GRT. See https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2016_06_16 for full details and links. The conference room link will be posted an hour before the meetup. GalaxyAdmins is a discussion group for Galaxy community members that administer Galaxy installations. Hope to see you (online) on Thursday, Dave Clements and Hans-Rudolf Hotz -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

2 1

fail to install pulsar on windows machine
by Jun Fan 15 Jun '16

15 Jun '16

Dear all, I used to utilize LWR on a windows machine to run windows-only tools. As recently I upgrade the Galaxy to the latest stable version 16_01, Galaxy indicated that no LwrJobRunner available. Therefore I had to install Pulsar. When I followed the instruction at https://pulsar.readthedocs.io/en/latest/install.html and failed. 1. From PyPI option: after executing pulsar-config and two files app.yaml and server.ini being generated, the command pulsar returns the error saying 'pulsar' is not recognized as an internal or external command, operable program or batch file. 2. From Source option: it failed at run.bat step and got the main error message as "ImportError: No module named grp". My python is 2.7.11 and in the python shell, the command "import grp" gives the same error. Any help is welcome Best regards! Jun

1 0

Infinite recursion on conda dependency manager
by Peter van Heusden 15 Jun '16

15 Jun '16

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

2 1

History is not up-to-date
by Rathert, Philipp, Dr. 15 Jun '16

15 Jun '16

Dear All, I have a problem with my histories. We are running the Docker galaxy stable version 16.04 and when I start a tool the history does not show that it is running. it is not specific for any tool but for all. however, something is running in the back 129.69.102.30 - - [14/Jun/2016:12:57:21 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A16.601Z HTTP/1.1" 200 - "http://129.69.102.42/ <http://129.69.102.42/> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 271|app: 0|req: 74/163] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:21 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A16.601Z => generated 2511 bytes in 33 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 2) 129.69.102.30 - - [14/Jun/2016:12:57:25 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A20.635Z HTTP/1.1" 200 - "http://129.69.102.42/ <http://129.69.102.42/> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 271|app: 0|req: 75/164] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:25 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A20.635Z => generated 2511 bytes in 29 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 1) 129.69.102.30 - - [14/Jun/2016:12:57:29 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A24.673Z HTTP/1.1" 200 - "http://129.69.102.42/ <http://129.69.102.42/> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 271|app: 0|req: 76/165] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:29 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A24.673Z => generated 2112 bytes in 30 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 0) 129.69.102.30 - - [14/Jun/2016:12:57:33 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A28.711Z HTTP/1.1" 200 - "http://129.69.102.42/ <http://129.69.102.42/> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 272|app: 0|req: 90/166] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:33 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A28.711Z => generated 2112 bytes in 32 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 0) 129.69.102.30 - - [14/Jun/2016:12:57:37 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A32.749Z HTTP/1.1" 200 - "http://129.69.102.42/ <http://129.69.102.42/> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 271|app: 0|req: 77/167] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:37 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A32.749Z => generated 2112 bytes in 27 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 3) I am not sure how to fix this and I am happy for any suggestion. Cheers, Philipp

3 2

Re: [galaxy-dev] how to get raw input from GUI
by Dooley, Damion 14 Jun '16

14 Jun '16

A general note, besides <sanitize> which sounds like a fine choice, a technique I've used where the form's input might have some wonky characters in it, including carriage returns, but these need to be received and processed via a command line, is to use encode(): $rules.encode('base64').replace('\n','') Then over in receiving python script Rules = rulesparam.decode('base64') D. >Message: 3 >Date: Mon, 13 Jun 2016 17:12:05 -0700 >From: Beginner TI <ruiwang.sz(a)gmail.com> >To: "galaxy-dev(a)lists.bx.psu.edu" <galaxy-dev(a)lists.bx.psu.edu> >Subject: [galaxy-dev] how to get raw input from GUI >Message-ID: > <CAPNcnp5B8uzQbAHLqA7ak4NMpQZ+CDitvNDg0J9ZS+bS5A06OQ(a)mail.gmail.com> >Content-Type: text/plain; charset="utf-8" > >Hi, > >I am working on a wrapper for gatk and including > > <repeat name="filters" title="filter names and expressions" >help="--filterName, --filterExpression"> > <param name="filter_name" type="text" value="" >title="Filter name to be included in the analysis" /> > <param name="filter_exp" type="data" value="" >title="Filter >expression to be included in the analysis" /> > </repeat> > >in it, however, when I reference it using > >${filter.filter_exp} > >it would translate 'FS > 30.0' into XXXFS __gt__ 30.0XXX > >is there a way that I could keep the original text string 'FS > 30.0'? I >did a quick lookup online but didn't see anything in cheetah's user guide >or other places. > >Thanks, >Rui

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galaxy-dev June 2016