can not run JChem base Installation on linux web server

User 773d472e7f

21-06-2012 08:46:09

I have installed JChem on a linux web server.


but the command line tools are not running eg:  jcman. This is the case for both a local development server where I can confirm the gui tools are working and also on a web vserver were I have no access to gui tools:
root@v14908:~/ChemAxon/JChem/bin# jcman -h
-bash: jcman: command not found.



Please advise my next step, Many thanks, Bernard.


here is the listing of the bin directory:




root@v14908:~/ChemAxon/JChem/bin# ls -lF
total 236
-rwxr-xr-x 1 root root 3977 Jun 12 10:03 bm*
-rwxr-xr-x 1 root root 3974 Jun 12 10:03 compr*
-rwxr-xr-x 1 root root 3974 Jun 12 10:03 config*
-rwxr-xr-x 1 root root 3978 Jun 12 10:03 count*
-rwxr-xr-x 1 root root 4090 Jun 12 10:03 creact*
-rwxr-xr-x 1 root root 3977 Jun 12 10:03 crview*
-rwxr-xr-x 1 root root 3973 Jun 12 10:03 cxcalc*
-rwxr-xr-x 1 root root 3970 Jun 12 10:03 cxtrain*
-rwxr-xr-x 1 root root 3978 Jun 12 10:03 enumerate*
-rwxr-xr-x 1 root root 3969 Jun 12 10:03 evaluate*
-rwxr-xr-x 1 root root 3986 Jun 12 10:03 exampleCount*
-rwxr-xr-x 1 root root 3977 Jun 12 10:03 fragment*
-rwxr-xr-x 1 root root 3985 Jun 12 10:03 fragstat*
-rwxr-xr-x 1 root root 3978 Jun 12 10:03 generatemd*
-rwxr-xr-x 1 root root 3973 Jun 12 10:03 generfp*
-rwxr-xr-x 1 root root 3980 Jun 12 10:03 hitstatistics*
-rwxr-xr-x 1 root root 3980 Jun 12 10:03 jarp*
-rw-r--r-- 1 root root   75 Jun 21 10:15 java.ini
-rwxr-xr-x 1 root root 4038 Jun 12 10:03 jcman*
-rwxr-xr-x 1 root root 3967 Jun 12 10:03 jcsearch*
-rwxr-xr-x 1 root root 3967 Jun 12 10:03 jcunique*
-rwxr-xr-x 1 root root 3977 Jun 12 10:03 jklustor*
-rwxr-xr-x 1 root root 4069 Jun 12 10:03 libmcs*
-rwxr-xr-x 1 root root 4063 Jun 12 10:03 license*
-rwxr-xr-x 1 root root 3991 Jun 12 10:03 markushview*
-rwxr-xr-x 1 root root 3970 Jun 12 10:03 mcs*
-rwxr-xr-x 1 root root 4100 Jun 12 10:03 metabolize*
-rwxr-xr-x 1 root root 3975 Jun 12 10:03 molconvert*
-rwxr-xr-x 1 root root 4013 Jun 12 10:03 moledit*
-rwxr-xr-x 1 root root 3990 Jun 12 10:03 molfragment*
-rwxr-xr-x 1 root root 3968 Jun 12 10:03 msketch*
-rwxr-xr-x 1 root root 3978 Jun 12 10:03 mspace*
-rwxr-xr-x 1 root root 3966 Jun 12 10:03 mview*
-rwxr-xr-x 1 root root 3983 Jun 12 10:03 nneib*
drwxr-xr-x 2 root root 4096 Jun 21 10:15 np/
-rwxr-xr-x 1 root root 3983 Jun 12 10:03 optimizemetrics*
-rwxr-xr-x 1 root root 3976 Jun 12 10:03 pmapper*
-rwxr-xr-x 1 root root 4144 Jun 12 10:03 react*
-rwxr-xr-x 1 root root 4013 Jun 12 10:03 redit*
-rwxr-xr-x 1 root root 3970 Jun 12 10:03 rgdecomp*
-rwxr-xr-x 1 root root 3986 Jun 12 10:03 rmap*
-rwxr-xr-x 1 root root 3985 Jun 12 10:03 rtest*
-rwxr-xr-x 1 root root 4030 Jun 12 10:03 scedit*
-rwxr-xr-x 1 root root 3975 Jun 12 10:03 screen3d*
-rwxr-xr-x 1 root root 3985 Jun 12 10:03 screeningoptimizer*
-rwxr-xr-x 1 root root 3975 Jun 12 10:03 screenmd*
-rwxr-xr-x 1 root root  626 Jun 12 10:03 setup*
-rwxr-xr-x 1 root root 4105 Jun 12 10:03 standardize*
-rwxr-xr-x 1 root root 4022 Jun 12 10:03 standedit*
-rwxr-xr-x 1 root root 4098 Jun 12 10:03 structurechecker*
-rwxr-xr-x 1 root root 3970 Jun 12 10:03 toxic*
-rwxr-xr-x 1 root root 4003 Jun 12 10:03 toxicView*
-rwxr-xr-x 1 root root 3989 Jun 12 10:03 toxiccalc*
-rwxr-xr-x 1 root root 3990 Jun 12 10:03 toxicophore*
-rwxr-xr-x 1 root root 3971 Jun 12 10:03 ward*


ChemAxon 61b4fee994

21-06-2012 09:00:43

Hello Bernard,


Is . added to your path? Could you try it by executing


./jcman -h


?


Regards,


Tamas

User 773d472e7f

21-06-2012 09:34:35

Hi Tamas


OK, this works with the "." 


....and I think I understand more...


When I cd into the ...\bin\ directory I need to add the "."


I now need to find the place where I set this ...\bin\ directory into PATH environment variable. Is this correct?


Thanks!


Bernard

ChemAxon 61b4fee994

21-06-2012 13:39:52

Hi,


You can add the "." to the path, so you can access every file in your current directory without the ./  prefix.


Or you can add ~/ChemAxon/JChem/bin to your path to access all commands from that directory even when your current directory is different.


You can add that to your path by the export command:


export PATH=$PATH:<added path>


You can also add this line to your .bash_profile file in your home directory to automatically use the new path after login.


Regards,


Tamas