rostlab / loctree3 Goto Github PK

According to the README file, it's necessary to "Download the 80% non-redundant blast database (big_80 * ) combining SWISS-PROT, TrEMBL and PDB from https://rostlab.org/rost-db-data/big/" is there way to run it without these files? The big_80* files sum together more than 18Gb.

Hello,
An error appeared when i used loctree3:

Resolving rostlab.org (rostlab.org)... 131.159.28.73
Connecting to rostlab.org (rostlab.org)|131.159.28.73|:21... failed: Connection refused.
loctree2 package data is missing from /usr/share/loctree2-data and automatic retrieval failed. Please download it from ftp://rostlab.org/free/loctree2-data-1.0.2.tar.gz and untar it to /usr/share/loctree2-data.
Since the download is restartable, you also can re-run this command '/home/manager/LocTree3/install/share/loctree3/loctree2data' to reattempt data download. The incomplete data file is in /tmp/loctree2-data-1.0.2.tar.gz.

but the link is unavailable
ftp://rostlab.org/free/loctree2-data-1.0.2.tar.gz

Thanks
Best Regards

• See older wiki on Rostlab.org

Note, the students don't have to do this! Only marked for the possible future.

Originally written by @amerello on obtaining reading access to the svn repo:

Hola Juanmi,
  tu sabes como podría obtener privilegios de lectura sobre este
repositorio svn+ssh://rostlab.org/mnt/project/subversion/loctree3/trunk/ ?

Muchas gracias.
Saludos,
Alejandro.

Hi,

Your Dockerfile of LocTree3 in README.md may not work properly, because of change the pass of NCBI BLAST.

I changed the Dockerfile as follows and "docker build" ran successfully, though I don't know this make LocTree3 analyze real data properly.

FROM ubuntu:14.04
RUN apt-get -y update && apt-get install -y wget unzip automake make libconfig-inifiles-perl pp-popularity-contest
RUN wget -q https://github.com/Rostlab/LocTree3/archive/develop.zip && unzip -q develop.zip
RUN cd LocTree3-develop && aclocal && autoconf && autoheader; automake --add-missing && ./configure && make && make install
RUN wget -q ftp://ftp.ncbi.nlm.nih.gov/blast/executables//blast+/2.7.1/ncbi-blast-2.7.1+-x64-linux.tar.gz && tar xf ncbi-blast-2.7.1+-x64-linux.tar.gz
RUN /bin/echo -e "[NCBI]\nData=/ncbi-blast-2.7.1+/data/" > ~/.ncbirc && /bin/echo -e "export PATH=$PATH:/ncbi-blast-2.7.1+/bin" >> ~/.bashrc

executing ./configure produces the following error:
config.status: error: cannot find input file: 'data/Makefile.in'
executing make afterwards fails.

This is just to tell you that I could successfully run the tool with the provided instructions (using the docker image). I just did a few fixes to the doc and put the links to the Elixir pages.

Important: Note that I changed the repo name from LocTree to LoctTree3 following the instruction of the original author, Tatyana Goldberg. You will have to change your remote links.

As last extra push, you could submit the docker image to Docker Hub. There is a rostlab org too. Optional! As you wish :)

Hi,
I want to know how to install the pp-popularity-contest packages in centos? I have google but all is for Debian or Ubuntu.