We’re logged in and have a build node with internet access, so lets get some programs on here!
Pitchfork is a nice installer for PacBio related software, and since I plan to run PBJelly on Hyak, we’re going to need it.
First, we clone the GitHub repo via
git clone firstname.lastname@example.org:PacificBiosciences/pitchfork.git pitchfork
which nets us an error stating:
Cloning into '/usr/lusers/seanb80/programs/pitchfork'... Warning: Permanently added the RSA host key for IP address '188.8.131.52' to the list of known hosts. Permission denied (publickey). fatal: Could not read from remote repository. Please make sure you have the correct access rights and the repository exists.
I know the repo exists, since I used it yesterday, so it’s an access thing. After a bit of googling, I realize that I forgot I had to add an SSH key for my GitHub account on the GitHub website. Oops.
ssh-keygen -t rsa -b 4096 -C "email@example.com"
to make the key pairs
ssh-add -k ~/.ssh/id_rsa2
to add the code to the list of active key pairs
to show the public key, which I copy in to GitHub via the directions found here starting at step 2.
We try the clone again and receive
Cloning into '/usr/lusers/seanb80/programs/pitchfork'... remote: Counting objects: 9046, done. remote: Total 9046 (delta 0), reused 0 (delta 0), pack-reused 9045 Receiving objects: 100% (9046/9046), 1.01 MiB | 0 bytes/s, done. Resolving deltas: 100% (4769/4769), done. [seanb80@n2185 pitchfork]$ ls bin LICENSE Makefile mk ports README.md settings.mk settings.mk.example
We installed something!
Then we switch to the legacy blasr version via
git checkout legacy_blasr
which gets us the error
[seanb80@n2185 pitchfork]$ make init make -f mk/init.mk init make: Entering directory `/gscratch/home/seanb80/programs/pitchfork' /gscratch/home/seanb80/programs/pitchfork/bin/checkSystem /gscratch/home/seanb80/programs/pitchfork/bin/checkCC gcc [ERROR] gcc version needs to be newer than or equal to 4.9 make: *** [sanity] Error 1 make: Leaving directory `/gscratch/home/seanb80/programs/pitchfork' /gscratch/home/seanb80/programs/pitchfork/bin/checkSystem /gscratch/home/seanb80/programs/pitchfork/bin/checkCC gcc [ERROR] gcc version needs to be newer than or equal to 4.9 make: *** [sanity] Error 1
What version of GCC are we running?
[seanb80@n2185 pitchfork]$ gcc --version gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4)
Hm… Time to test out the yum package manager
[seanb80@n2185 pitchfork]$ yum install devtoolset-3-gcc-c++ Loaded plugins: fastestmirror Repodata is over 2 weeks old. Install yum-cron? Or run: yum makecache fast You need to be root to perform this command. [seanb80@n2185 pitchfork]$ sudo yum install devtoolset-3-gcc-c++ bash: sudo: command not found
Hah. We don’t even have access to sudo on a build node. That’s an issue!
Found a workaround here