metassembler / Discussion / General Discussion: I'm trying to make it run, but I think it does not compile

Salvador Espada-Hinojosa - 2016-11-25

hi,
I'm in a MacOSX 10.10 and when I follow the README instructions I don't manage to make it work. I downloaded the "Metassembler.1.5.tar.gz" file, and unzipped it. I moved it to my Applications folder. I checked that I have all dependencies (MUMmer, bowtie2, samtools...). When I type in Terminal in the Metassembler directory "make install" I get this outcome:
"
mkdir /Applications/Metassembler/bin
cd /Applications/Metassembler/GAGE; /Applications/Xcode.app/Contents/Developer/usr/bin/make all
/usr/bin/sed -e 's?/bin/bash?/bin/sh?g' \ -e 's?__GAGE_DIR?/Applications/Metassembler/GAGE?g' \ gage.sh > /Applications/Metassembler/bin/gage
chmod 755 /Applications/Metassembler/bin/gage
"
In the "bin/" folder I only see one binary file, "gage".

When I try to run the example "Sample" as indicated in README, I get this message:
"
./Metassemble_script.sh: line 35: ../../bin/metassemble: No such file or directory
"

Could you please help me to get it running?

Thanks a lot!

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- Alejandro Hernandez Wences - 2016-11-27
  
  Hi,
  
  Try installing it by typing:
  make Scr
  make scripts
  This will avoid installing the GAGE program
  
  Then try the sample data again to see if it is correctly installed. If this
  doesn't work please
  send us all the output from make, the output you posted seems to be
  incomplete?
  
  On Fri, Nov 25, 2016 at 3:57 PM, Salvador Espada-Hinojosa salvae@users.sf.net wrote:
  
  hi,
  I'm in a MacOSX 10.10 and when I follow the README instructions I don't
  manage to make it work. I downloaded the "Metassembler.1.5.tar.gz" file,
  and unzipped it. I moved it to my Applications folder. I checked that I
  have all dependencies (MUMmer, bowtie2, samtools...). When I type in
  Terminal in the Metassembler directory "make install" I get this outcome:
  "
  mkdir /Applications/Metassembler/bin
  cd /Applications/Metassembler/GAGE; /Applications/Xcode.app/
  Contents/Developer/usr/bin/make all
  /usr/bin/sed -e 's?/bin/bash?/bin/sh?g' \ -e 's?__GAGE_DIR?/Applications/Metassembler/GAGE?g'
  \ gage.sh > /Applications/Metassembler/bin/gage
  chmod 755 /Applications/Metassembler/bin/gage
  "
  In the "bin/" folder I only see one binary file, "gage".
  
  When I try to run the example "Sample" as indicated in README, I get this
  message:
  "
  ./Metassemble_script.sh: line 35: ../../bin/metassemble: No such file or
  directory
  "
  
  Could you please help me to get it running?
  
  Thanks a lot!
  
  I'm trying to make it run, but I think it does not compile
  https://sourceforge.net/p/metassembler/discussion/general/thread/f0d0ff2d/?limit=25#edd3
  
  Sent from sourceforge.net because you indicated interest in
  https://sourceforge.net/p/metassembler/discussion/general/
  
  To unsubscribe from further messages, please visit
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  alternate
  
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Nate Port - 2017-08-03

Hi, I've run into this same issue, where only the GAGE binary is placed in the bin folder.

Erics-MacBook-Pro:Metassembler MartensLab$ make
mkdir /Applications/Metassembler/bin
cd /Applications/Metassembler/GAGE; /Applications/Xcode.app/Contents/Developer/usr/bin/make all
/usr/bin/sed -e 's?/bin/bash?/bin/sh?g' \ -e 's?__GAGE_DIR?/Applications/Metassembler/GAGE?g' \ gage.sh > /Applications/Metassembler/bin/gage
chmod 755 /Applications/Metassembler/bin/gage

[bin directory appears with only gage in it]

To install without installing the GAGE program, did you mean to run make in the src folder and then in the scripts folder?

Erics-MacBook-Pro:bin MartensLab$ make Scr
make: No rule to make target Scr'. Stop. Erics-MacBook-Pro:Metassembler MartensLab$ make Src make:Src' is up to date.
Erics-MacBook-Pro:Metassembler MartensLab$ make scripts
make: `scripts' is up to date.

Erics-MacBook-Pro:Metassembler MartensLab$ cd src
Erics-MacBook-Pro:src MartensLab$ make
CEstat.cpp -c -o CEstat.o
make: CEstat.cpp: No such file or directory
make: [CEstat.o] Error 1

Erics-MacBook-Pro:src MartensLab$ cd ..
Erics-MacBook-Pro:Metassembler MartensLab$ cd Scripts/
Erics-MacBook-Pro:Scripts MartensLab$ make
cp RepGAGE.py /Applications/Metassembler/Scripts/RepGAGE
chmod 755 /Applications/Metassembler/Scripts/RepGAGE
cp RepMetassem.py /Applications/Metassembler/Scripts/RepMetassem
chmod 755 /Applications/Metassembler/Scripts/RepMetassem
cp RepStats.py /Applications/Metassembler/Scripts/RepStats
chmod 755 /Applications/Metassembler/Scripts/RepStats
cp RepREAPR.py /Applications/Metassembler/Scripts/RepREAPR
chmod 755 /Applications/Metassembler/Scripts/RepREAPR
cp RepCEGMA.py /Applications/Metassembler/Scripts/RepCEGMA
chmod 755 /Applications/Metassembler/Scripts/RepCEGMA
e 's?/usr/bin/perl -w? -w?g' \ splitscafffa.pl > /Applications/Metassembler/Scripts/splitscafffa
/bin/sh: e: command not found
make: [splitscafffa] Error 127 (ignored)
chmod 755 /Applications/Metassembler/Scripts/splitscafffa
e 's?/usr/bin/perl -w? -w?g' \ stats.pl >/Applications/Metassembler/Scripts/stats
/bin/sh: e: command not found
make: [stats] Error 127 (ignored)
chmod 755 /Applications/Metassembler/Scripts/stats
cp seqLengths.py /Applications/Metassembler/Scripts/seqLengths
chmod 755 /Applications/Metassembler/Scripts/seqLengths

[nothing new has appeared in bin]

Thanks for your help!

*

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- Alejandro Hernandez Wences - 2017-08-03
  
  Hi,
  
  Could you post the entire output for the first time you tried "make
  install" on the root directory of the package?
  
  This will give me a better hint of what could be going on.
  
  Thanks.
  
  On Wed, Aug 2, 2017 at 9:45 PM, Nate Port nateport@users.sf.net wrote:
  
  Hi, I've run into this same issue, where only the GAGE binary is placed in
  the bin folder.
  
  Erics-MacBook-Pro:Metassembler MartensLab$ make
  mkdir /Applications/Metassembler/bin
  cd /Applications/Metassembler/GAGE; /Applications/Xcode.app/
  Contents/Developer/usr/bin/make all
  /usr/bin/sed -e 's?/bin/bash?/bin/sh?g' \ -e 's?__GAGE_DIR?/Applications/Metassembler/GAGE?g'
  \ gage.sh > /Applications/Metassembler/bin/gage
  chmod 755 /Applications/Metassembler/bin/gage
  
  [bin directory appears with only gage in it]
  
  To install without installing the GAGE program, did you mean to run make
  in the src folder and then in the scripts folder?
  
  Erics-MacBook-Pro:bin MartensLab$ make Scr
  make: No rule to make target Scr'. Stop. Erics-MacBook-Pro:Metassembler
  MartensLab$ make Src make:Src' is up to date.
  Erics-MacBook-Pro:Metassembler MartensLab$ make scripts
  make: `scripts' is up to date.
  
  Erics-MacBook-Pro:Metassembler MartensLab$ cd src
  Erics-MacBook-Pro:src MartensLab$ make
  CEstat.cpp -c -o CEstat.o
  make: CEstat.cpp: No such file or directory
  make: [CEstat.o] Error 1
  
  Erics-MacBook-Pro:src MartensLab$ cd ..
  Erics-MacBook-Pro:Metassembler MartensLab$ cd Scripts/
  Erics-MacBook-Pro:Scripts MartensLab$ make
  cp RepGAGE.py /Applications/Metassembler/Scripts/RepGAGE
  chmod 755 /Applications/Metassembler/Scripts/RepGAGE
  cp RepMetassem.py /Applications/Metassembler/Scripts/RepMetassem
  chmod 755 /Applications/Metassembler/Scripts/RepMetassem
  cp RepStats.py /Applications/Metassembler/Scripts/RepStats
  chmod 755 /Applications/Metassembler/Scripts/RepStats
  cp RepREAPR.py /Applications/Metassembler/Scripts/RepREAPR
  chmod 755 /Applications/Metassembler/Scripts/RepREAPR
  cp RepCEGMA.py /Applications/Metassembler/Scripts/RepCEGMA
  chmod 755 /Applications/Metassembler/Scripts/RepCEGMA
  e 's?/usr/bin/perl -w? -w?g' \ splitscafffa.pl >
  /Applications/Metassembler/Scripts/splitscafffa
  /bin/sh: e: command not found
  make: [splitscafffa] Error 127 (ignored)
  chmod 755 /Applications/Metassembler/Scripts/splitscafffa
  e 's?/usr/bin/perl -w? -w?g' \ stats.pl >/Applications/Metassembler/
  Scripts/stats
  /bin/sh: e: command not found
  make: [stats] Error 127 (ignored)
  chmod 755 /Applications/Metassembler/Scripts/stats
  cp seqLengths.py /Applications/Metassembler/Scripts/seqLengths
  chmod 755 /Applications/Metassembler/Scripts/seqLengths
  
  [nothing new has appeared in bin]
  
  Thanks for your help!
  
  *
  
  I'm trying to make it run, but I think it does not compile
  https://sourceforge.net/p/metassembler/discussion/general/thread/f0d0ff2d/?limit=25#a706
  
  Sent from sourceforge.net because you indicated interest in
  https://sourceforge.net/p/metassembler/discussion/general/
  
  To unsubscribe from further messages, please visit
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  - Nate Port - 2017-08-03
    
    Hi Alejandro,
    
    This is all the output I get from running 'make install' in the root 'Metassembler' directory the first time (I did a clean install to verify):
    
    mkdir /Applications/Metassembler/bin
    cd /Applications/Metassembler/GAGE; /Applications/Xcode.app/Contents/Developer/usr/bin/make all
    /usr/bin/sed -e 's?/bin/bash?/bin/sh?g' \ -e 's?__GAGE_DIR?/Applications/Metassembler/GAGE?g' \ gage.sh > /Applications/Metassembler/bin/gage
    chmod 755 /Applications/Metassembler/bin/gage
    
    Like the OP I am also running this on a MacBook Pro OSX 10.10.5.
    
    If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

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I'm trying to make it run, but I think it does not compile