I am trying to install mothur from source, since it seems to be the only way to have the most recent version of it in ubuntu 12.04.
I’ve changed the makefile line:
#if you are a linux user use the following line
CXXFLAGS += -mtune=native -march=native
But when I run: “make”, at some point the following message appears:
g++ -O3 -mtune=native -march=native -DBIT_VERSION -DRELEASE_DATE="\"3/31/2015\"" -DVERSION="\"1.35.1\"" -DUSE_READLINE -I. -I calculators/ -I chimera/ -I classifier/ -I clearcut/ -I commands/ -I communitytype/ -I datastructures/ -I metastats/ -I randomforest/ -I read/ -I svm/ -c -o wilcox.o wilcox.cpp
cd uchime_src && ./mk && mv uchime .. && cd ..
/bin/sh: 1: ./mk: Permission
I’ve already tried to run with sudo make, but the same thing happens. Any ideas?
Thanks in advance.
Have you tried running our prebuilt executable, Mothur.cen_64.zip, https://github.com/mothur/mothur/releases?
It looks like the permissions are not quite right on the makefile for the uchime source. Can you check on them?
Johns-iMac:mothur sarahwestcott$ cd source
Johns-iMac:source sarahwestcott$ cd uchime_src
Johns-iMac:uchime_src sarahwestcott$ ls -l
total 832
-rw-r–r-- 1 sarahwestcott staff 1095 Mar 12 12:44 addtargets2.cpp
…
-rwxr-xr-x 1 sarahwestcott staff 1052 Mar 12 12:44 mk
…
-rw-r–r-- 1 sarahwestcott staff 7234 Mar 12 12:44 writechhit.cpp
What are you seeing for permissions on the file?
This also may be helpful, http://askubuntu.com/questions/310404/permission-denied-error-when-compiling-fortran-code-in-netbeans-7-3-1-on-ubuntu.
Hi!
When I run ls -l in uchime_src, I get:
total 393
-rw------- 1 joana joana 1095 Mar 31 19:04 addtargets2.cpp
-rw------- 1 joana joana 14948 Mar 31 19:04 alignchime.cpp
-rw------- 1 joana joana 8720 Mar 31 19:04 alignchimel.cpp
-rw------- 1 joana joana 275 Mar 31 19:04 allocs.h
-rw------- 1 joana joana 570 Mar 31 19:04 alnheuristics.h
-rw------- 1 joana joana 8204 Mar 31 19:04 alnparams.cpp
-rw------- 1 joana joana 1245 Mar 31 19:04 alnparams.h
-rw------- 1 joana joana 2258 Mar 31 19:04 alpha2.cpp
-rw------- 1 joana joana 70910 Mar 31 19:04 alpha.cpp
-rw------- 1 joana joana 1473 Mar 31 19:04 alpha.h
-rw------- 1 joana joana 1971 Mar 31 19:04 chainer.h
-rw------- 1 joana joana 2198 Mar 31 19:04 chime.h
-rw------- 1 joana joana 597 Mar 31 19:04 counters.h
-rw------- 1 joana joana 4440 Mar 31 19:04 diagbox.h
-rw------- 1 joana joana 5094 Mar 31 19:04 dp.h
-rw------- 1 joana joana 1030 Mar 31 19:04 evalue.h
-rw------- 1 joana joana 9261 Mar 31 19:04 fractid.cpp
-rw------- 1 joana joana 1890 Mar 31 19:04 getparents.cpp
-rw------- 1 joana joana 1005 Mar 31 19:04 globalalign2.cpp
-rw------- 1 joana joana 4993 Mar 31 19:04 help.h
-rw------- 1 joana joana 187 Mar 31 19:04 hspfinder.h
-rw------- 1 joana joana 2041 Mar 31 19:04 hsp.h
-rw------- 1 joana joana 3493 Mar 31 19:04 make3way.cpp
-rw------- 1 joana joana 1052 Mar 31 19:04 mk
-rw------- 1 joana joana 6947 Mar 31 19:04 mx.cpp
-rw------- 1 joana joana 10100 Mar 31 19:04 mx.h
-rw------- 1 joana joana 6111 Mar 31 19:04 myopts.h
-rw------- 1 joana joana 42443 Mar 31 19:04 myutils.cpp
-rw------- 1 joana joana 7758 Mar 31 19:04 myutils.h
-rw------- 1 joana joana 1019 Mar 31 19:04 orf.h
-rw------- 1 joana joana 3248 Mar 31 19:04 out.h
-rw------- 1 joana joana 3039 Mar 31 19:04 path.cpp
-rw------- 1 joana joana 885 Mar 31 19:04 path.h
-rw------- 1 joana joana 6700 Mar 31 19:04 searchchime.cpp
-rw------- 1 joana joana 6654 Mar 31 19:04 seqdb.cpp
-rw------- 1 joana joana 2231 Mar 31 19:04 seqdb.h
-rw------- 1 joana joana 674 Mar 31 19:04 seq.h
-rw------- 1 joana joana 1594 Mar 31 19:04 setnucmx.cpp
-rw------- 1 joana joana 10203 Mar 31 19:04 sfasta.cpp
-rw------- 1 joana joana 2043 Mar 31 19:04 sfasta.h
-rw------- 1 joana joana 447 Mar 31 19:04 svnmods.h
-rw------- 1 joana joana 5 Mar 31 19:04 svnversion.h
-rw------- 1 joana joana 2803 Mar 31 19:04 timers.h
-rw------- 1 joana joana 5392 Mar 31 19:04 timing.h
-rw------- 1 joana joana 3014 Mar 31 19:04 tracebackbit.cpp
-rw------- 1 joana joana 1920 Mar 31 19:04 uc.h
-rw------- 1 joana joana 4646 Mar 31 19:04 uchime_main.cpp
-rw------- 1 joana joana 121 Mar 31 19:04 ultra.h
-rw------- 1 joana joana 1818 Mar 31 19:04 usort.cpp
-rw------- 1 joana joana 7260 Mar 31 19:04 viterbifast.cpp
-rw------- 1 joana joana 1984 Mar 31 19:04 windex.h
-rw------- 1 joana joana 7234 Mar 31 19:04 writechhit.cpp
I'm new in ubuntu, is there any problem with the permissions?
Thanks!
Looking at the permissions, you don’t have execute permissions on the mk file. I just edited my post as you were replying. Did you try the prebuilt executable version for Linux? If you don’t want to use that option, to change the permissions on the mk file try this:
Johns-iMac:uchime_src sarahwestcott$ chmod 755 mk
Johns-iMac:uchime_src sarahwestcott$ ls -l mk
-rwxr-xr-x 1 sarahwestcott staff 1052 Mar 12 12:44 mk
The prebuilt function doesn’t seem to be working with me because although I install the v1.35, mothur runs version 1.22.2-2.
I did run chmod 755 mk, but the permissions are still the same… (I think the problem is in the partition format)
Ok, thank you a LOT!
The problem was that I was trying to install mothur in a NFTS formatted partition, which doesn’t seem to let the permissions be changed. I did solved the problem installing mothur in other partition.
I am glad you were able to get things going. If you downloaded the prebuilt version and are running version 1.22, then you likely have an older version of mothur in your path. You can find it by running:
sarahwestcott$ which mothur
Alternatively, if you want to run the prebuilt version you just downloaded you can cd into the mothur directory and run:
mothur sarahwestcott$ ./mothur