Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-06-15

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All times shown according to UTC.

Time Nick Message
07:33 viklund joined #bioperl
08:48 viklund joined #bioperl
13:30 nErVe joined #bioperl
13:30 nErVe anybody here.
15:35 deafferret hi
16:01 viklund joined #bioperl
17:15 perl_splut joined #bioperl
19:42 nErVe joined #bioperl
21:10 rbuels deafferret: does pyrimidine know about the proposed Bio::Graphics-ectomy at YAPC?
22:08 deafferret rbuels: no idea. I never got the details of the proposal
22:08 deafferret i don't think.... I'm a few hundred personal email behind
22:09 rbuels hah.
22:34 nErVe joined #bioperl
22:47 nErVe can I run a -----  ::     system ("mptopdf *.mp");
22:51 deafferret sure?
23:04 nErVe its does not run
23:05 rbuels nErVe: is mptopdf in your path?
23:05 rbuels (and what does this have to do with bioperl)?
23:06 nErVe well because i m using it for phylogenetic trees
23:06 nErVe i m using the cafe program
23:07 nErVe "nErVe: is mptopdf in your path?" No clue what that means
23:07 nErVe please elaborate
23:08 deafferret linux?
23:08 rbuels nErVe: what operating system are you using?
23:09 nErVe ubuntu
23:10 deafferret type 'which mptopdf'
23:12 nErVe ok I got the path so its like a shebang
23:12 nErVe am i correct when i say that
23:12 rbuels not really
23:13 rbuels do you mean you are putting the full path to mptopdf in the call to system() ?
23:13 rbuels such as '/usr/local/bin/mptopdf'?
23:13 nErVe #!/usr/bin/mptopdf is this the way I would write it in my perl script
23:13 nErVe at the start
23:13 deafferret I'm suggesting you use full paths in your system call
23:14 deafferret so system("/usr/bin/mptopdf /other/path/to/files/*.mp")
23:15 nErVe ahh interesting
23:15 rbuels if you type 'echo $PATH' at the command line, that shows all the paths that are searched for executable files if you type a command without adding the full path
23:17 nErVe well I tried what you told me """system("/usr/bin/mptopdf /other/path/to/files/*.mp")""" didnt work
23:17 nErVe i wonder why
23:17 deafferret unless you get cron involved, or any other insanity
23:18 deafferret didn't work?
23:18 rbuels it depends on where you have mptopdf installed
23:18 rbuels and where you got it
23:18 rbuels (did you install it?)
23:18 deafferret nopaste your code   http://sial.org/pbot/
23:18 nErVe well i installed by sudo apt-get install context
23:19 rbuels then mptopdf should be in /usr/bin/mptopdf, hopefullyu
23:20 nErVe http://scsys.co.uk:8002/29808
23:20 nErVe the script runs correctly its  script to run another script
23:21 deafferret I'm suggesting absolute paths. so not 'cafeFile_001/'
23:21 deafferret everything should start with /
23:22 nErVe so are you talking specifically for the mptopdf line
23:22 nErVe or all lines
23:22 deafferret what does "didn't work" mean? did it eat your cat? did it produce errors? what were the errors?
23:23 nErVe well the process runs and keeps running..creates the files to the folders moves the file to the folder but doent not runt he last command
23:23 deafferret i'm suggesting you use absolute paths for everything. programs, files, etc
23:23 deafferret the command with the # in front?
23:24 nErVe ok I will look into that suggestion you have given
23:24 perl_splut you can get rid of the if-then-else by using sprintf
23:25 perl_splut $index = sprintf("%04d", $i);
23:25 nErVe I tried the sprintf function but could into the format I needed it to be
23:26 nErVe so I stuck with the other one
23:26 deafferret %02d is what you have there
23:26 nErVe I must say i really need to work hard on my coding I am getting a lot of criticisms
23:27 deafferret i hope you find them constructive  :)
23:27 deafferret i get a dozen or more a day. makes me a better coder
23:27 perl_splut two things that might screw up the system call.
23:27 nErVe coming back to the mptopdf thing please.....and yes definitely
23:27 perl_splut the path variable and the current working directory
23:28 perl_splut if this was launched from a Cronjob, then it might not have the correct CWD setup to use the relative paths that you have for the file locations
23:29 nErVe its not a cronjob
23:31 perl_splut system ("/usr/bin/mptopdf cafeFile_001/results_001/pdf_001/*.mp");
23:31 perl_splut something off about that line
23:32 perl_splut e.g. all your attempts are to make it 0001 and you are using 001
23:32 perl_splut so it is going into a non-existant directory structure
23:33 nErVe well I corrected tat now and am running the script get back to you in a sec
23:35 nErVe well same thing again have to kill the process
23:36 nErVe does everything except the last mptopdf
23:36 perl_splut which last one?
23:36 perl_splut you have one line commented out
23:36 nErVe can i paste the last line here please
23:37 perl_splut you can try
23:37 nErVe system ("/usr/bin/mptopdf mptopdf /home/vikram/Desktop/Long_Project/new_t​est/6_Species/CAfe/temp/cafeFile_0001/r​esults_0001/pdf_0001/results_0001.mp");
23:37 perl_splut why are you calling mptopdf twice?
23:37 nErVe i tried the other way also
23:37 nErVe by a single call
23:38 nErVe I got the same result as earlier
23:38 perl_splut you are calling "/usr/bin/mptopdf mptopdf"
23:38 perl_splut that is probably messing it up
23:39 nErVe system ("/usr/bin/mptopdf /home/vikram/Desktop/Long_Project/new_t​est/6_Species/CAfe/temp/cafeFile_0001/r​esults_0001/pdf_0001/results_0001.mp");
23:39 nErVe I did this also but I got the same results as earlier
23:39 perl_splut and be aware that linux/unix is CASE-SENSITIVE. CAfe and cafe aren't the same thing
23:41 perl_splut and just for fits and shiggles. Try running that command outside of perl and see if it works.
23:41 perl_splut .   /usr/bin/mptopdf /home/vikram/Desktop/Long_Project/new_​test/6_Species/CAfe/temp/cafeFile_0001​/results_0001/pdf_0001/results_0001.mp
23:43 nErVe i got a no file name matches error
23:46 perl_splut did you copy the "."? if so, don't. I was using that so I could paste a line with a leading /
23:46 deafferret can you 'ls' that path and see files?
23:47 deafferret ls /home/vikram/Desktop/Long_Project/new_​test/6_Species/CAfe/temp/cafeFile_0001​/results_0001/pdf_0001/results_0001.mp
23:47 nErVe ok that command does run
23:47 nErVe the one given by perl_splut
23:48 nErVe btw
23:48 nErVe bash: ./usr/bin/mptopdf: No such file or directory when the "." is included
23:49 nErVe bash: ./usr/bin/mptopdf: No such file or directory ----  ERROR when the "." is included
23:49 perl_splut as expected
23:49 perl_splut since you changed the path when including the .
23:49 nErVe so my error is.?
23:49 deafferret take the period out
23:50 perl_splut that was your error when trying it from the command-line
23:50 perl_splut as I said. I put the "." at the beginning as / is the begining of a command to IRC
23:50 nErVe well when i run it without the "." it runs fine
23:50 deafferret perl_splut: '/ /blah'
23:54 nErVe as i said i tried the code suggested by perl_splut without the "." it runs fine
23:54 nErVe and gives me the output
23:59 nErVe any suggestions..??

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