Closed Toliman06 closed 5 years ago
thanks,
new pre realese 3.1 take your comment into account
I am also not sure, but there is some problems with the INSTALL_from_source.md: we define out bin directory at the begining (BIN_DIR=$DIR/bin) but after, in the script, we are using commandes with "/home/frogs/bin/". Might not be $BIN_DIR?
/home/frogs/bin/ is used in: 10) Needlall 6.6.0.0, for FROGS Affiliation_OTU 11) MAFFT 7.407, for FROGS Tree
Your are right for section 10) Needleall.
For section 11) MAFFT this is an example, since you need to write the value of your BIN_DIR variable, you can't use "$BIN_DIR" in the Makefile.
If you wait few days conda receipt will be availbale, and FROGS will also be available in the Toolshed. This will be the adviced way to intall FROGS.
I will use the conda version, but I wanted to install FROGS by myself (as you know I tried for a long time...)
Just one last thing: in the Test FROGS sections, the code
sh test.sh ~/FROGS <NB_CPU> <JAVA_MEM> <OUT_FOLDER>
must be
sh test.sh ~/FROGS-3.1.0/ <NB_CPU> <JAVA_MEM> <OUT_FOLDER>
and it's finally work... failed:
~/FROGS-3.1.0/test$ sh test.sh ~/FROGS-3.1.0/ 4 4 ./test_results/
Step preprocess : Flash lundi 7 janvier 2019, 14:39:23 (UTC+0100)
Step preprocess : Vsearch lundi 7 janvier 2019, 14:39:54 (UTC+0100)
Step clustering lundi 7 janvier 2019, 14:40:29 (UTC+0100)
Step remove_chimera lundi 7 janvier 2019, 14:43:08 (UTC+0100)
Step filters lundi 7 janvier 2019, 14:44:16 (UTC+0100)
Step ITSx lundi 7 janvier 2019, 14:44:23 (UTC+0100)
Step affiliation_OTU lundi 7 janvier 2019, 14:44:26 (UTC+0100)
Step affiliation_postprocess lundi 7 janvier 2019, 14:44:45 (UTC+0100)
Step clusters_stat lundi 7 janvier 2019, 14:44:45 (UTC+0100)
Step affiliations_stat lundi 7 janvier 2019, 14:44:45 (UTC+0100)
Step biom_to_tsv lundi 7 janvier 2019, 14:44:47 (UTC+0100)
Step biom_to_stdBiom lundi 7 janvier 2019, 14:44:47 (UTC+0100)
Step tsv_to_biom lundi 7 janvier 2019, 14:44:47 (UTC+0100)
Step tree : mafft lundi 7 janvier 2019, 14:44:47 (UTC+0100)
test.sh: 257: test.sh: tree.py: Permission denied
Error in tree : mafft
then
/FROGS-3.1.0/tools/tree$ ll
total 52
drwxrwxr-x 2 dunoyerd dunoyerd 4096 janv. 4 15:03 ./
drwxrwxr-x 25 dunoyerd dunoyerd 4096 janv. 4 15:03 ../
-rwxrwxr-x 1 dunoyerd dunoyerd 454 janv. 4 15:03 test.sh*
-rw-rw-r-- 1 dunoyerd dunoyerd 13958 janv. 4 15:03 tree.py
-rw-rw-r-- 1 dunoyerd dunoyerd 22482 janv. 4 15:03 tree_tpl.html
chmod +x solved the problem... anyone else had this problem? (then, it's working fine know, even if I had to copy RDPtools .jar from a previous installation...)
for the FROGS test command line, the correction applied is:
sh test.sh ../ <NB_CPU> <JAVA_MEM> <OUT_FOLDER>
as we recommand to move to $FROGS_test in the first step.
for the tree.py rigths, I never noticed that! that's strange, so thanks for your test.
In section 5) swarm 2.2.2, for FROGS Clustering, there is a "-" missing in the "./bin/swarm -version" command line (--version) ;)