Allow for own/other samtools/bowtie2 executables.

[hjmangalam]

I run a cluster that has its own, well-integrated samtools and bowtie2. It would be convenient if using your supplied tools (thanks for the thought, but..) was optional, and the scripts just looked for the executables on the PATH. Or you supplied static executables. Your exes are built with Intel's TBB which we don't have, and also some other libs that aren't found. And your GLIBC requirements are too modern for our Devonian kernel.

[snayfach]

That's a good suggestion that I'll look into. In the meantime, can you try replacing the binaries located in /path/to/MIDAS/bin/Linux with the ones that work for your system? Also, you can try downloading the latest version of the software which has binaries that might work better for you.

[hjmangalam]

On Tuesday, March 6, 2018 11:03:50 PM PST Stephen Nayfach wrote:

That's a good suggestion that I'll look into. In the meantime, can you try replacing the binaries located in /path/to/MIDAS/bin/Linux with the ones that work for your system? Also, you can try downloading the latest version of the software which has binaries that might work better for you.

That's what I ended up doing in the end (overwriting yours). It was a simple, but somewhat confusing fix, since I was trying to modify the PATH to look for OUR binaries, but the path seems to be hard-wired to use yours.

Also, for most application distributions, having a 'setup.py' in the root distribution dir strongly implies that running the 'python setup.py install' will install the distro. Once that's done, pip says it's installed:

Tue Mar 06 15:18:14 root@hpc-login-1-2:~ 1001 $ module load enthought_python Tue Mar 06 15:18:22 root@hpc-login-1-2:~ 1002 $ pip list --format=columns | grep -i midas

but of course it's not - it requires the involvement of the MIDAS distribution dir. You describe this later on in the installation doc, but 'setup.py' is such a standard mechanism of installing code, you might add a warning that gets printed to remind users that it's not quite set up for use yet.

Just my 2 cents...

hjm

-- Harry Mangalam, Research Computing, Rm 225 MSTB, UC Irvine [m/c 2225] / 92697 Google Voice Multiplexer: (949) 478-4487 415 South Circle View Dr, Irvine, CA, 92697 [shipping] XSEDE 'Campus Champion' - ask me about your research computing needs. Map to MSTB[1]| Map to Data Center Gate[2]

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[snayfach]

Thanks for the suggestions!

[boris-dimitrov]

I had a similar problem on a brand new Ubuntu 18 AMI in AWS EC2 and worked around like so:

cd MIDAS/bin/Linux
for f in *; do ln -sf `which $f` $f; done

That was after installing bowtie, samtools, and vsearch on my system as per the instructions.