How can I run 'mpileup' using Bioperl ?
When trying to run mpileup using Bio::Tools::Run::Samtools , I am getting 'mpileup' is not registered. What am I doing wrong? Any pointers towards the right direction are appreciated... thank you guys.....
The short answer is you cannot run mpileup using BioPerl-Run because, as your error message describes, that command does not appear to be listed as one available to samtools. You might want to raise this issue on the bioperl-listserv, and hopefully someone will add this feature.
Related
I apologize if this has been answered in another post, I can't seem to find it if it has. Anyway, I have built a back end utility for a fellow streamer friend of mine but I can't seem to figure out what I'm doing wrong when it comes to deploying it. This is a project that will be expanded on in the future, and possibly have more windows form projects. So here is what I am running into (With Pictures):
Here is my solution explorer with the projects:
When I go to build the deployment I've tried making all the projects "outputs" and got this error. Thinking it was there were too many Project Outputs I changed it to where the startup project would be the output and the others would be either source or content files. Still got these errors. Here is the File System Setup:
And when I go to run the build to create the deployment, here are the errors I receive:
I don't know/don't see what I am doing wrong here and would very much appreciate a point in the right direction. Thank you all so much in advance.
Check your updates. I remember there is an option to review or check the status of latest updates.
I found this article about that issue but it looks like a general error with updates or the installation
It is not too long but maybe it does not help. I hope it helps, good luck
I am trying to build nsf/ntf via command line, I am trying to follow this link Headless Designer . Every thing seems in the documentation very obvious.
But even if I have added 'DESIGNER_AUTO_ENABLED=true' in notes.ini the command explained in the documentation doesn't seems working.
Error:Command or Option is not recognized.
Hope someone has tried this.
Any kind of advice and suggestion are appreciated.
Thank you.
I know that this question has been posted multiple times. And I have done my research but still was left clueless. So please bear with me but I wanted to see if someone can offer more direct help,
I am using the latest Python xy distribution
https://code.google.com/p/pythonxy/
I launched an ipython session and tried to write a simple fibonacci function, after doing load_ext cythonmagic. But ran into the above error. I also set the env. variable VS90COMNTOOLS to equal %VS100COMNTOOLS%, as some posts suggested. That did not fix it, what else can I do to fix the error?
Thanks
I'm trying to profile my C code with gprof. I'm compiling .a library with -pg option and compiling executable also with -pg and with this .a library.
Running. Getting gmon.out. Viewing it using Eclipse. And all I getting is something like showed at screenshot bellow.
I assume there should be some functions instead those addresses.
Can somebody tell me how to fix it?
Thanks in advance,
- Ilya.
I just checked gmon.out with gprof using command line instead of Eclipse and it appeared that there is no any ?? and 0xaddresses. So I assume that it is some kind of Eclipse viewer issue. Thanks for paying attention to this. I'll also try all tool that you suggested.
I am having some trouble uploading code to my Seeeduino ADK (essentially a Arduino Mega 2560) using Eclipse. Basically, this thread explains my problem. Sometimes I get a series of timeouts using the Arduino IDE upload, which is usually fixed by removing and re-inserting the USB. Unfortunately enough, this does not help fix the problem in Eclipse.
I have been trying to do the upload using AVRdude via the command line (I even tried the "hacky" solution in the last comment of the above thread), but to no avail. This is the line I am using for this:
"%AVR_DUDE%" -pm2560 -cstk500v2 -P\\.\%COMM_PORT% -b115200 -F -V -D - Uflash:w:"%HEX_FILE%":a -C"%AVR_DUDE_CONF%"
Which gives me:
avrdude.exe: stk500v2_ReceiveMessage(): timeout
I know the above batch variables are OK, because AVRdude runs correctly (but then it times out). If anyone has any ideas or tips that could help me with my uploading I would greatly appreciate it. Thanks beforehand.
EDIT: As it turns out, the reason for this may be that the Arduino IDE sends a reset to the board before uploading, something which the Eclipse AVR plugin does not do. I will test this and write a uploading perl script, but I am fairly certain this is the problem.
Your suspicion is correct. The Arduino IDE uses a patched version of AVRDude to pulse the DTR line and reset the board before each upload. For some reason, some people have had difficulty getting the right command line parameters to replicate this on the Mega2560. I've had the same problem myself - ATMega328's work with no problem, but the 2560 needs to be reset manually.
There's some further explanation and tips for possibly getting it working here (check the comments too): http://false.ekta.is/2011/05/avrdude-5-10-arduino-mega-2560-command-line-uploading/
Check out the detail here... http://false.ekta.is/2011/05/avrdude-5-10-arduino-mega-2560-command-line-uploading/
If using avrdude > version 5.1 change the programmer to -cwiring
This will reset the chip first