Where to download platypus?

[E Ra]

Hi, 

Would you know where to get the latest stable version of Platypus. The link in well.ox.ac.uk seems not work.

https://www.well.ox.ac.uk/research/research-groups/lunter-group/lunter-group/platypus-a-haplotype-based-variant-caller-for-next-generation-sequence-data

Any help is appreciated.

Thanks

[Andy Rimmer]

I'm not sure what the correct link is now. Copying Gerton Lunter, who should be able to point you to the right place.

Another option is to download the latest code from Github: https://github.com/andyrimmer/Platypus

Kind regards,

Andy

--
You received this message because you are subscribed to the Google Groups "Platypus Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to platypus-user...@googlegroups.com.
To view this discussion on the web, visit https://groups.google.com/d/msgid/platypus-users/bed1cb08-179b-4d31-92c6-21cbfe1a193c%40googlegroups.com.

--

Dr Andrew (Andy) Rimmer

[E Ra]

Hello Andy,

Thank you for your answers. Could you help me to install it, please? I had the error message below when I tried to install it through your github page.  I have python 3.7.3 and cython 0.29.13. 

I got this error after run the "make" command line.

Thank you,

E Ra

echo 'Building Platypus'

Building Platypus

cd src; python setup.py build

running build

running build_py

running build

running build_py

running build

running build_py

running build

running build_py

running build

running build_py

running build

running build_py

running build

running build_py

running build

running build_py

running build

running build_ext

cythoning cython/htslibWrapper.pyx to cython/htslibWrapper.c

/16tbdata/myprograms/miniconda3/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /16tbdata/myprograms/Platypus/src/cython/htslibWrapper.pxd

  tree = Parsing.p_module(s, pxd, full_module_name)

 

Error compiling Cython file:

------------------------------------------------------------

...

        If _open is called on an existing bamfile, the current file will be

        closed and a new file will be opened.

        """

        if mode not in ("r", "rb", "rbh"):

            raise StandardError, "invalid file opening mode `%s`" % mode

                 ^

------------------------------------------------------------

 

cython/htslibWrapper.pyx:151:18: undeclared name not builtin: StandardError

building 'htslibWrapper' extension

gcc -pthread -B /16tbdata/myprograms/miniconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/16tbdata/myprograms/miniconda3/include/python3.7m -c cython/htslibWrapper.c -o build/temp.linux-x86_64-3.7/cython/htslibWrapper.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function

cython/htslibWrapper.c:1:2: error: #error Do not use this file, it is the result of a failed Cython compilation.

 #error Do not use this file, it is the result of a failed Cython compilation.

  ^~~~~

error: command 'gcc' failed with exit status 1

Makefile:34: recipe for target 'platypus' failed

make: *** [platypus] Error 1

On Fri, Sep 13, 2019 at 2:21 AM Gerton Lunter <gerton...@well.ox.ac.uk> wrote:

Hi - we’re moving the pages, and the download page is temporarily unavailable, apologies for that.  Please use the Github page as Andy indicated for now.

Best wishes

Gerton

[E Ra]

I also tried to install it through conda. It seems work but I could not locate the Platypus.py in the system.

Thank you

conda config --add channels conda-forge
conda install platypus-opt

which Platypus.py

# I have nothing