Re^6: Can't run Clustalw through Bioperl

Replies are listed 'Best First'.
Re^7: Can't run Clustalw through Bioperl by Marshall (Canon) on Mar 14, 2016 at 05:25 UTC
$ENV{CLUSTALDIR} = 'C:\Program Files (x86)\ClustalW2'; Please look very carefully at the path. On my current machine, I have both /Program Files (x86)/ and just /Program Files/ directories. Almost all my Program Files are in the "plain" directory. Just one program lives in /Program Files (x86)/. I can't say for sure whether this will help or not, but it is an anomaly that I noticed on this particular machine.	[reply]
Re^8: Can't run Clustalw through Bioperl by GrandFather (Saint) on Mar 14, 2016 at 05:35 UTC
The (x86) variant is where 32 bit applications live. The "plain" directory contains 64 bit apps. It's a pretty good bet that the OP's application is 32 bit. Premature optimization is the root of all job security	[reply]
Re^9: Can't run Clustalw through Bioperl -- filesystem redirection? by Discipulus (Canon) on Mar 14, 2016 at 08:27 UTC
Another victim of file system redirection? If the promtp is 64bit and the perl is 64bit there is no chance to view the 32bit part of the installation. If just one component of the chain is 32bit there is no chance to view what the OS consider to be only 64bit related. If you need you can use the special path `sysnative` See mines: Re: Cannot execute external process: Win32 Win64 SysWOW64 and System32 redirection and Re: Reading subkeys from registry -- evil registry redirection? L* There are no rules, there are no thumbs.. Reinvent the wheel, then learn The Wheel; may be one day you reinvent one of THE WHEELS.	[reply] [d/l] [select]
Re^9: Can't run Clustalw through Bioperl by Marshall (Canon) on Mar 15, 2016 at 09:34 UTC
Well the machine that I saw this on is a Win XP laptop! No 64 bit here! By definition, all apps are 32 bit. I was just wondering if there is some path mismatch between a newer version that installs to the (x86) directory and an older installation that installed into the "plain" directory. I am quite sure that you are correct about 64 bit installations on a 64 bit machine. But I am also sure that in the pre-64 bit era the same thing happened. This (x86) thing is new.	[reply]
Re^7: Can't run Clustalw through Bioperl by 1nickt (Canon) on Mar 14, 2016 at 05:05 UTC
--->System couldn't file Clustalw Isn't the file supposed to be called `clustalw.exe`? Does the error message really mention a file with a capital letter in the name? I fear you have some basic file path/permission problem, with which I could scarcely help from afar, even if I knew Windows. The way forward always starts with a minimal test.	[reply] [d/l]
Re^7: Can't run Clustalw through Bioperl by poj (Abbot) on Mar 14, 2016 at 17:13 UTC
What is the name of the file you double click on. Is it `clustalw2.exe` ? poj	[reply] [d/l]
Re^8: Can't run Clustalw through Bioperl by dimitris852 (Acolyte) on Mar 14, 2016 at 20:21 UTC
yeap the file is `clastalw2.exe` and NOT `clustalw.exe` as written on perl error.I was cleary searching for wrong file. If I `C:\> where clustalw2.exe` I get eventually: `C:\Program Files (x86)\ClustalW2\clustalw2.exe`So I can find the executable by command line. But `'C:\Program Files (x86)\ClustalW2'` is the same i use from the beggining, and even though I ve put `ENV{CLUSTALDIR}` on the script and add it to Windows Path variable i have this error..	[reply] [d/l] [select]
Re^9: Can't run Clustalw through Bioperl by poj (Abbot) on Mar 14, 2016 at 20:38 UTC
Try creating a shortcut `clustalw.exe` to `C:\Program Files (x86)\ClustalW2\clustalw2.exe` or add this line to your code `$Bio::Tools::Run::Alignment::Clustalw::PROGRAM_NAME = 'clustalw2';` poj	[reply] [d/l] [select]
Re^10: Can't run Clustalw through Bioperl by dimitris852 (Acolyte) on Mar 14, 2016 at 22:46 UTC
Re^11: Can't run Clustalw through Bioperl by Anonymous Monk on Mar 14, 2016 at 23:14 UTC
Some notes below your chosen depth have not been shown here
Re^10: Can't run Clustalw through Bioperl by dimitris852 (Acolyte) on Mar 14, 2016 at 21:03 UTC