Can someone point me to an installation guide for Megan on Linux?

User Questions
1

Is there a simple guide to install Megan6 on a Linux server?

cheers

Julian

1 Like
2

Download the installer MEGAN_Community_unix_6_8_14.sh from MEGAN6 download.

Open a terminal.
Change to the directory containing the installer (using the cd command)
Ensure that the installer is executable:

chmod u+x MEGAN_Community_unix_6_8_14.sh

Launch the installer in console mode:

./MEGAN_Community_unix_6_8_14.sh -c

Follow the prompted instructions.

3

Hi, Daniel. Thank you for your simple step to install MEGAN. I installed the MEGAN_unix_5_11_3.sh successfully using command “sh MEGAN_unix_5_11_3.sh -c”, but then I failed when I was trying to install the MEGAN6 vertion, it quitted automaticlly after showing"Unpacking JRE, Starting Installer…". Fortunately, this problem have been solved, after I changed the folder name. So I send it here for reference, and it might be helpful for others.

4

Did you ever figure this out? I am trying to install Megan on our supercomputer, but do not know where to start.

5

These steps should work:

  1. Download the latest installer:

wget https://software-ab.cs.uni-tuebingen.de/download/megan6/MEGAN_Community_unix_6_24_12.sh

  1. Run the installer in interactive, non-GUI mode:

chmod u+x MEGAN_Community_unix_6_24_12.sh
./MEGAN_Community_unix_6_24_12.sh -c

  1. Download the mapping file:
    wget https://software-ab.cs.uni-tuebingen.de/download/megan6/megan-map-Feb2022.db.zip
  2. Unzip the mapping file:

unzip megan-map-Feb2022.db.zip

  1. Run the DAA meganizer using the Linux “X virtual frame buffer” program:

xvfb-run --auto-servernum --server-num=1 <Path-to-MEGAN-Installation>/tools/daa-meganizer -mdb megan-map-Feb2022.db -i <Your Input Files>

This will “meganize” your DAA files (be sure to run DIAMOND with option -f 100 to generate DAA format), if you used DIAMOND as your aligner and NCBI-nr as database.

Once the files have been meganized, you have multiple options:

  1. If your server permits, login using “ssh -Y” (in in some way that supports “X forwarding”) and then run MEGAN directly on the server.
  2. Consider using megan-server, a program that we provide in the tools directory of MEGAN. It can serve files from the server to instances of MEGAN running on other computers, e.g. your personal computer. Details can be found in our preprint.
  3. The tools directory contains a number of command-line programs for analyzing the files and extracting data from them
  4. If you are running the Ultimate Edition, then you can write scripts to run MEGAN on the data on the server
  5. Download the files to your personal computer and open in MEGAN.
6

I tried to install MEGAN in a server, but it did not work.

$ sh MEGAN_Community_unix_6_24_19.sh -c
Unpacking JRE …
Starting Installer …
Picked up JAVA_TOOL_OPTIONS: -Xmx2g
[0.848s][warning][os,thread] Failed to start thread “GC Thread#40” - pthread_create failed (EAGAIN) for attributes: stacksize: 1024k, guardsize: 4k, detached.
[0.849s][error ][gc,task ] GC(0) Failed to create worker thread
[0.859s][warning][os,thread] Failed to start thread “G1 Conc#1” - pthread_create failed (EAGAIN) for attributes: stacksize: 1024k, guardsize: 4k, detached.
[0.860s][error ][gc,task ] GC(1) Failed to create worker thread
[0.864s][warning][os,thread] Failed to start thread “G1 Conc#1” - pthread_create failed (EAGAIN) for attributes: stacksize: 1024k, guardsize: 4k, detached.
[0.864s][error ][gc,task ] GC(1) Failed to create worker thread

There is insufficient memory for the Java Runtime Environment to continue.
Native memory allocation (malloc) failed to allocate 16 bytes for AllocateHeap

Let me know if you have any suggestions about Megan installation.