These are chat archives for nextflow-io/nextflow

22nd
Sep 2016
Paolo Di Tommaso
@pditommaso
Sep 22 2016 06:44
@mes5k very good, I will make more tests on my side. If everything is fine I will include in the next release
Mokok
@Mokok
Sep 22 2016 07:59
hi @pditommaso
any update about using nextflow on windows ? mingw ?
Paolo Di Tommaso
@pditommaso
Sep 22 2016 08:00
never tested, you may want to try mingw or the new Windows 10 Linux subsystem
If you do, I will invite you to write a guest post on the nextflow blog :)
Mokok
@Mokok
Sep 22 2016 08:03
ok, i'll try out with mingw and hope to keep you positively aware ;)
Paolo Di Tommaso
@pditommaso
Sep 22 2016 08:03
great thanks
Mokok
@Mokok
Sep 22 2016 08:24

well, first of all the "curl -fsSL get.nextflow.io | bash" cmd print :
many:
/d/Users/.../.../nextflow: line 352: printf: missing unicode digit for \U
and then:
Error occurred during initialization of VM
agent library failed to init: instrument
Failed to find Premain-Class manifest attribute in C:\Users\bajulie.nextflow\framework\0.22.0\nextflow-0.22.0-one.jar

any idea ?

Paolo Di Tommaso
@pditommaso
Sep 22 2016 08:27
uh
is Java installed and running that env ?
Mokok
@Mokok
Sep 22 2016 08:28
both jre or jdk 7x32 7x64 8x64
Paolo Di Tommaso
@pditommaso
Sep 22 2016 08:29
it looks that the paths are messed up
Mokok
@Mokok
Sep 22 2016 08:29
but ... any chance that having java on C: and my nextflow dir on D: cause it ?
well, i'll try on C: jsut to be sure
(btw, using bitbash 's mingw64)
Paolo Di Tommaso
@pditommaso
Sep 22 2016 08:30
no it seem that it tries to interpret the \U in C:\Users\.. as a unicode char
Mokok
@Mokok
Sep 22 2016 08:30
it can try but i'm pretty sure it wont succed :D
Paolo Di Tommaso
@pditommaso
Sep 22 2016 08:31
no idea how deal with that, the path should be in the unix format i.e./ and not \
Mokok
@Mokok
Sep 22 2016 08:31
i'll try on cywin then, i case it comes from mingw
Paolo Di Tommaso
@pditommaso
Sep 22 2016 08:32
do you not have a Win10 OS ?
Mokok
@Mokok
Sep 22 2016 08:33
nop win 7
Paolo Di Tommaso
@pditommaso
Sep 22 2016 08:33
ok
Mokok
@Mokok
Sep 22 2016 08:49
good and bad news
Paolo Di Tommaso
@pditommaso
Sep 22 2016 08:50
:/
Mokok
@Mokok
Sep 22 2016 08:51
there is only one news :D
talk to my manager about this little problem (i wasn't aware that running nextflow on windows was a new requirement), said we'll use another executor in this specific case.
So...it's not a problem anymore, but i won't give you any information about how we could achieve that as it's not a need anymore ^^
Paolo Di Tommaso
@pditommaso
Sep 22 2016 08:52
out of curiosity, what is the alternative executor ?
Mokok
@Mokok
Sep 22 2016 08:52
don't know for now
Paolo Di Tommaso
@pditommaso
Sep 22 2016 08:52
ok, enjoy
Mokok
@Mokok
Sep 22 2016 08:54
thanks anyway, don't forget to write it big and bold in a patch note if you find a way to allow nextflow execution on windows os :D
Paolo Di Tommaso
@pditommaso
Sep 22 2016 08:55
ok, I will try it soon or later
Mokok
@Mokok
Sep 22 2016 08:57
good luck then, have a good day
Paolo Di Tommaso
@pditommaso
Sep 22 2016 08:57
same there
Jason Byars
@jbyars
Sep 22 2016 20:08

@pditommaso just a quick follow up from yesterday. I get an error/assert on any permutation of file(''), file(null), file('not real'). I can do HOTSPOTS = params.hotspots ? file(params.hotspots) : null; instead, but then if I do

HOTSPOTS = params.hotspots ? file(params.hotspots) : null;
process foo {
  input: 
  file HOTSPOTS

  script:
  """
  blah blah blah
  """
}

if HOTSPOTS is null, the process hangs. It's not a big deal, I can live with an absolute path for that one reference file. I'm just curious about the concept of a process with optional reference files.

Paolo Di Tommaso
@pditommaso
Sep 22 2016 20:11
um
file('not real') or file('DUMMY') should work
yes, it hangs because it's waiting a file
Jason Byars
@jbyars
Sep 22 2016 20:15
makes sense. I'm looking into the issue with file()
Jason Byars
@jbyars
Sep 22 2016 22:43
ok, I get it now. I just need to do HOTSPOTS = params.hotspots ? file(params.hotspots) : file('nothing'); It's only a problem when file() interprets the input as null