After getting the license info. I go to designated site and sign in as Academic_User, with password. For all of Rossetta releases, all I see are files with the .gz extension. Downloading these and using gunzip on linux, just gives a binary file-not even executable--Actually need source code anythow. What am I missing? I would have expected files with .tgz, for which I can get the source code (or , I guess the binaries plus source as bundle) to compile. I would like to try and use SnugDock, which I sense from other Forum responses, is only available with 2.3.1. But this issue with the .gz extension prevents me from even checking this. I've downloaded 3.3 a year ago--I think it was .tgz and have it compiled--but can't remember what the actual extension was at the download site at the time. Is SnugDock in version 3.7 somewhere ?
You mention gunzip but not tar. They should be tarballs - .tar.gz or .tgz. Decompress and untar them with tar -xvzf whatever.tgz .
If you mean that you did try tar, and not gunzip, and you still get garbage, let me know exactly which one you tried and I'll be happy to check if it's corrupted.
Snugdock should be in 3.7, or the most recent weekly.
I do not get tarballs--all I get is a file with .gz extension not .tgz. For example I click on "Rosetta 3.7 source", and save to my downloads dir. and what I get is rosetta_src_3.7_bundle.gz. I tried to email firstname.lastname@example.org but the mail came back undeliverable. I'll try email@example.com
They're just going to send you back here.
I assume the page we are talking about is https://www.rosettacommons.org/downloads/academic/3.7/, and the file we are talking about is rosetta_src_3.7_bundle.tar.gz? Does it match this md5sum (taken from the md5 hashes list on the same page)?:
Well, when I click on "MD5.checksum ot files" I see "701b66d69132f1641d4cc35ed38a6786 rosetta_src_2016.32.58837_bundle.tgz" in the list--If that is what is meant by "match", then yes, I think.
Actually, I just found a copy of rosetta_bin_linux_2016.32.58837_bundle.tar (Rosetta 3.2) laying around that I must have downloaded last August, and which appears to have SnugDock. I suppose I can get started with that for now.
I meant for you to calculate the md5sum of whatever file you've downloaded. Like so:
>$ md5sum testfile
Yes, md5sum rosetta_src_3.7_bundle.tar.gz gives
which matches what is given on the download page.
I downloaded it locally to check.
-> % gmd5sum rosetta_src_3.7_bundle.tgz
~> & tar -xvzf rosetta_src_3.7_bundle.tgz
-> % ll rosetta_src_2016.32.58837_bundle
drwxr-xr-x@ 25 smlewis staff 850 Aug 10 08:06 demos
drwxr-xr-x@ 36 smlewis staff 1224 Aug 10 08:06 documentation
drwxr-xr-x@ 9 smlewis staff 306 Aug 10 08:06 main
drwxr-xr-x@ 43 smlewis staff 1462 Aug 10 08:06 tools
This builds fine (at least it starts up fine), so the file is OK on my end. What exactly do you get after untarring?
Again, the file I get just has the .gz extension not .tgz.
However,If I do
> tar -xvzf rosetta_src_3.7_bundle.gz
So, I do get a list of all the files and subdirectoires expected, but afterward, do not get the directory created named rosetta_src_3.7_bundle
I can't duplicate the extension changing problem.
That looks more or less like the files you should have; naviagate to main/source and compile it normally. Is that subdirectory not present, or does it not compile....? Can you not find the binaries after compiling?
Oh I see. The tar commnd was writing all the files/subdir's to "rosetta_src_2016.32.58837_bundle" while I was expecting and looking for a dir named "rosetta_src_3.7_bundle" and "rosetta_src_2016.32.58837_bundle" directory already existed for months. Also, I thought the 32 in the name stood for version 3.2 which was confusing me. Anyhow,
I believe this is resolved.
The 32 is from week 32 - Rosetta 3.7 is the week 32 release; we provide 'numbered' releases for the convienence of those who have to convince third parties (sysadmins, etc) to update Rosetta for them, and have an easier time doing so with numbered releases. My apologies for the confusion! I will suggest that we rename the files and re-tar them instead of just renaming the tarball next time.