Torsten Seemann

parsnp now in brewsci/bio packaging system

1

I ported the code to `libmuscle` and `parsnp` ``` brew install brewsci/bio/parsnp ``` Will install v1.2 from source.

Now in homebrew

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``` brew install brewsci/bio/swipe ```

``` brew install brewsci/bio/quip ```

ant builds, but nothing in dist/ folder

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``` cd kestrel-1.0.1 ant copyresources: [mkdir] Created dir: /home/tseemann/tmp/kestrel-1.0.1/build/classes/edu/gatech/kestrel/img ls dist (empty) bin/ has hierarchy of .class files ```

Lots of warnings about std::auto_ptr

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This may not be critical but happens a lot with C++ builds: ``` ../dlib/dlib/matrix/../smart_pointers/shared_ptr.h:299:18: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr& r ^ In file included from /home/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/memory:81:0, from...

static_all 1.1.3 seer/kmds segfault at end

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It prints the help, then it pauses for 1 second, then it dumps core. The `kmds` command does the same thing. Downloaded from: https://github.com/johnlees/seer/releases/download/v1.1.3/seer_v1.1.3_static_all.tar.gz The same happens with the `_static`...

Global REFID="hCoV-19/Wuhan/WH04/2020|EPI_ISL_406801|2020-01-05"

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Was wondering if using a single "common.inc" file for things like 'hCoV-19/Wuhan/WH04/2020|EPI_ISL_406801|2020-01-05' Would be good? Or even `export REFID=` in the main script to the scripts/ inherit it? can use...

See https://github.com/DerrickWood/kraken2

Newick parser error - "Couldnt find tip for seq1" ?

2

``` $ cat test.fa >seq1 ATCT >seq2 ATCG >seq3 ATAT $ cat test.nw (seq1:0.1,(seq2:0.7,seq3:0.8)); Reading sequences from test.fa ... Read 3 sequences First sequence is:seq1 Last sequence is:seq3 Reading tree...