Windows version of pysam
530 views
Skip to first unread message
Stuart Hay
Nov 7, 2017, 1:27:12 PM11/7/17
to Pysam User group
Hello,
I am an employee at Cincinnati Childrens. I am currently working on a project that requires a windows version of pysam, so our group developed one. We were wondering if we could upload it to pypi, as it is needed for our current project. It is not allowed without the author's permission. Where could I contact someone about this?
Thank you,
Stuart Hay
Andreas Heger
Nov 10, 2017, 11:47:38 AM11/10/17
to pysam-us...@googlegroups.com
Hi Stuart,
that is really good news. I know there are a lot of people wanting a
Windows version.
Can your changes be integrated into the pysam main branch? I would then
be happy to make it part of the pysam release cycle. This way all
packages in pysam-pypi would be synced in their versions. Or if
windows/unix are fully incompatible, could it live as a branch in the
pysam repository? That way, bugfixes and new features could be
cherry-picked from the master branch to the windows one.
If it can't be merged, I am not sure what the best solution is. I think
the general expectation is that a pypi package is derived from a single
code base. A way forward could be to create a separate project (such as
pysam-windows) on pypi, which you are welcome to do.
My preferred solution of course would be to keep a single code base.
Best wishes,
Andreas
> --
> You received this message because you are subscribed to the Google
> Groups "Pysam User group" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to pysam-user-gro...@googlegroups.com
> <mailto:pysam-user-gro...@googlegroups.com>.
> For more options, visit https://groups.google.com/d/optout.
that is really good news. I know there are a lot of people wanting a
Windows version.
Can your changes be integrated into the pysam main branch? I would then
be happy to make it part of the pysam release cycle. This way all
packages in pysam-pypi would be synced in their versions. Or if
windows/unix are fully incompatible, could it live as a branch in the
pysam repository? That way, bugfixes and new features could be
cherry-picked from the master branch to the windows one.
If it can't be merged, I am not sure what the best solution is. I think
the general expectation is that a pypi package is derived from a single
code base. A way forward could be to create a separate project (such as
pysam-windows) on pypi, which you are welcome to do.
My preferred solution of course would be to keep a single code base.
Best wishes,
Andreas
> You received this message because you are subscribed to the Google
> Groups "Pysam User group" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to pysam-user-gro...@googlegroups.com
> <mailto:pysam-user-gro...@googlegroups.com>.
> For more options, visit https://groups.google.com/d/optout.
Randy Harr
Mar 3, 2021, 7:29:51 PM3/3/21
to Pysam User group
Did anything ever happen with this? I would like to start incorporating pysam into our tool release. Have no problem doing something that Cincinnati Children's does as custom either; if we can distribute to end users.
We support the DTC 30x WGS testing market. And are platform agnostic (support Win10, MacOS and Linux). Mostly Python code. See https://wgsextract.github.io/
We have been supplying Win10 executables of htslib, samtools, bwa, etc for 1.5 years now. That is about 50% of our users. Could do more in the tool with pysam. I have no problems compiling the htslib tools now on Win10 (2.5 years ago when we started was a different story). We only provide 64 bit execs now though (used to support 32 bit). CRAM manipulation of WGS results on 32 bit just does not work. I tried to native compile pysam by overriding the MS Visual C++ to Cygwin64 gcc (how we make releases for htslib now), but just could not come up with the right combination or find where I could easily remove the direction to VisualC++ that is hardcode in. Please let me know. Would love to just be in BioConda but a slight majority of our users are on Win10 machines which they seem to refuse to support.
We have been supplying Win10 executables of htslib, samtools, bwa, etc for 1.5 years now. That is about 50% of our users. Could do more in the tool with pysam. I have no problems compiling the htslib tools now on Win10 (2.5 years ago when we started was a different story). We only provide 64 bit execs now though (used to support 32 bit). CRAM manipulation of WGS results on 32 bit just does not work. I tried to native compile pysam by overriding the MS Visual C++ to Cygwin64 gcc (how we make releases for htslib now), but just could not come up with the right combination or find where I could easily remove the direction to VisualC++ that is hardcode in. Please let me know. Would love to just be in BioConda but a slight majority of our users are on Win10 machines which they seem to refuse to support.
teepean47
Mar 15, 2022, 5:19:19 PM3/15/22
to Pysam User group
With the following as a guide it is possible to compile pysam with a recent version of MSYS2/MinGW-w64.
Reply all
Reply to author
Forward
0 new messages