Hi Laura, On 10 April 2012 22:25, Laura Scearce <flitr...@gmail.com> wrote:
> I am using Linux version 2.6 and python version 2.6.6 (gcc version 4.4.5). > What distribution of Linux? (Ubuntu, Debian, Centos or something else?) I followed the instructions and it seemed to work (see below error > messages). > > [snip...] > compilation terminated. > error: Setup script exited with error: command 'gcc' failed with exit > status 1 > That means gcc is likely not installed. GCC is the GNU C compiler. On Linux, Python modules written in C needs GCC to be able to install. I imagine BioPython is written in C, which would explain why it wants GCC during installation. On Ubuntu/Debian, you can fix the lack of GCC by using the following command: sudo apt-get install build-essential This will install the "build-essential" package which includes GCC and a bunch of other development tools. (If you're not using Debian or Ubuntu or a distribution based on Debian the above command won't work.) > *I also tried it in the directory Downloads, because this is where the > easyinstall was downloaded to. Same message. > After installing "easy_install" into your Python environment, the originally downloaded file is redundant/irrelevant to the functioning of easy_install, so the folder you're in doesn't actually matter. Which is why you get the same message. :) > > Then I tried downloading Biopython from > http://pypi.python.org/pypi/biopython > I downloaded > biopython-1.59.tar.gz<http://pypi.python.org/packages/source/b/biopython/biopython-1.59.tar.gz#md5=c83b26cc1bc2b2ecdce28c1b5e49110d>. > and extracted it to the folder BLAST-SW in my Documents folder. > > Here is what I tried: > debbie@debbie-VirtualBox:~/Documents/BLAST-SW$ sh biopython-1.59.tar.gz > sh: Can't open biopython-1.59.tar.gz > debbie@debbie-VirtualBox:~$ sh biopython-1.59.tar.gz > sh: Can't open biopython-1.59.tar.gz > debbie@debbie-VirtualBox:~/Documents/BLAST-SW$ sh biopython-1.59 > *This had no error message, but I think that Biopython is not installed > because: > >>> import Bio > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > ImportError: No module named Bio > A .tar.gz file is not a shellscript file or bundle. It is a type of archive file, and to extract it you need to use the "tar" command or a GUI tool that can read tar.gz files. (I'm a tad puzzled as you seem to understand this file needs to be extracted, yet the commands you issue implies you seem to think you can run the file as-is?) Normally you'd use a command like this: tar -zxvf biopython-1.59.tar.gz ... which will extract the the biopython-1.59.tar.gz file into the current folder. In case the files in the archive are not in a subfolder it's therefore a bit safer to create your own targer folder first, then extract from within this new folder, e.g. something like: mkdir biopython cd biopython tar -zxvf ../biopython-1.59.tar.gz Finally having briefly scanned the biopython download page, I want to point out that there are Biopython packages available for Ubuntu/Debian systems, so if you're using one of these Linux distributions you should preferentially use Synaptic (or another Debian package tool like apt-get or aptitude) to install BioPython as this will be a lot less grief. Walter
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