Question: Problem in execution of the commands in HMMER
0
gravatar for ambika_dudhate
2.1 years ago by
ambika_dudhate0 wrote:

Hello everyone,

i am new to bioinformatics and being a biologist i dont have much knowledge about commands and command based softwares, i have installed Hmmer-3.1b2.cygwin64 on windows 10 by using cygwin. following the steps:

% tar zxf hmmer-3.1b2.cygwinn64.tar.gz
% cd hmmer-3.1b2
% ./configure
% make
% make check

i think No errors were there and all the steps were fine as all check were saying OK , but after installation when for a trial i use the default command (> hmmbuild globins4.hmm tutorial/globins4.sto ) to perform the hmmbuild, the error was showing as command not found, screenshot attached which shows the path of cygwin and error My computer is in Japanese so the command not found error is in Japanese language

Please help me with this HMMER is very important for my research

Thank you in advance

hmmer hmmscan hmmbuild • 2.2k views
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by ambika_dudhate0

I can't install even I read the instructor. (Same Win10 system with cygwin)

My problem is that once I "./configure", it says :

configure: Configuring HMMER for your system. checking build system type... x86_64-unknown-cygwin checking host system type... x86_64-unknown-cygwin configure: Full HMMER source distribution - using full configuration checking for gcc... no checking for cc... no checking for cl.exe... no configure: error: in /hmmer-3.1b2-cygwin64': configure: error: no acceptable C compiler found in $PATH Seeconfig.log' for more details

How can I fix this?

ADD REPLYlink written 2.0 years ago by weiyuanchen20150

Please use unix subsystem for Windows 10 (https://docs.microsoft.com/en-us/windows/wsl/about ) if you want to do this on Windows 10. You will have significantly less trouble. Do you also have enough memory to be able to run HMMER?

ADD REPLYlink written 2.0 years ago by genomax76k

Thank you "genomax", I can install now by following this () The problem is that I didn't install the some essential functions.

I know it is better to run with unix subsystem for Windows 10, but I am not sure if I can understand how to use it I am new to use this as well...(to this website, too)

BTW, I have 8GB RAM on my computer, is that enough?

ADD REPLYlink written 2.0 years ago by weiyuanchen20150

Did you not install a compiler for cygwin? This is just the first link that showed up in a search to install gcc.

ADD REPLYlink written 2.0 years ago by genomax76k
1
gravatar for arnstrm
2.1 years ago by
arnstrm1.7k
Ames, IA
arnstrm1.7k wrote:

Although you installed the program, you didn't add them to PATH. PATH is like a address where the machine looks for when you call the program/executable like hmmbuild. One easy way to fix this is rather than calling hmmbuild you can provide the complete path for the executable, like /cygwindrive/c/cygwin64/home/user/hmmer-3.1b2.cygwin64/hmmbuild. This way the system doesn't have to search anywhere and the executable is called directly.

Also, the correct way to fix is adding the programs to PATH as follows:

PATH=$PATH:/cygwindrive/c/cygwin64/home/user/hmmer-3.1b2.cygwin64

You can add this to your ~/.bashrc or run it every time you want to run HMMER.

(on the side note, if you're using Win10, you should probably enable the Linux subsystem rather than emulating the linux like environment with Cygwin. It is much more feature rich and will provide you the real linux experience)

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by arnstrm1.7k

Hello, I am trying to use hmmer and I have the same problem as above, saying that the hmmbuild function is not found. I tried to add the path as you indicated but it is not working https://ibb.co/fCNhpN5

I am a complete beginner in programming, may it be possible to have your insight on the problem I am facing ?

Sorry for the bother and thank you in advance for your help

ADD REPLYlink modified 11 months ago • written 11 months ago by halteman0

Hello halteman,

Try to add the PATH upto "bin" folder

May be it will work

Good luck

ADD REPLYlink written 11 months ago by ambika_dudhate0
0
gravatar for ambika_dudhate
2.1 years ago by
ambika_dudhate0 wrote:

hello arnstrm, Thank you very much for reply I have added the PATH (by using advance system setting and manually adding the PATH in the path variable) but when i am executing the command echo$PATH it says /home/User/hmmer-3.1b2-cygwin64 - no such file or directoryscreenshot of the command echo$PATH

ADD COMMENTlink written 2.1 years ago by ambika_dudhate0
1

From the location where the hmmbuild is located, run the pwd -P command. Copy down the path and use that for adding to the $PATH. I wasn't completely sure where the hmmbuild in your system was located and assumed it was right! Hope this helps!

ADD REPLYlink written 2.1 years ago by arnstrm1.7k
0
gravatar for ambika_dudhate
2.1 years ago by
ambika_dudhate0 wrote:

thank you very much it worked well now i can use the command!!

ADD COMMENTlink written 2.1 years ago by ambika_dudhate0
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