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&, 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<TValue, TSpec>&, 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<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)’:
> 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)’:
> 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)’:
> SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef ‘T
