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Old 08-04-2014, 07:03 AM   #21
simobioinfo
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Thank you and excuse me but I registered to the site just few minutes ago. The command function even if I have also to digit
export PATH="$PATH:/bin"
I have another question: How do I make permanent this command? When I close terminal, the problem returns.
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Old 08-04-2014, 07:11 AM   #22
dpryan
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You just need to edit ~/.bashrc
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Old 08-04-2014, 07:57 AM   #23
simobioinfo
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Do I have to do these changes as root? If I digit ~/.bashrc, I heve the following message: permission denied
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Old 08-04-2014, 08:12 AM   #24
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If you are logged into your user account then you should be able to edit your .bashrc file by using an appropriate text editor such as pico/nano by doing

Code:
$ pico ~/.bashrc
After you add the export line the .bashrc remember to save the file and then source it.

Code:
$ source ~/.bashrc
or you could log out and then log back in again (when the .bashrc would be re-read). Using "source" command allows you to read the profile without having to log out then in.

Last edited by GenoMax; 08-04-2014 at 08:16 AM.
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Old 08-04-2014, 12:25 PM   #25
simobioinfo
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Thank you so much... my shell now is functional.
Now I have to add bowtie2 to path, which was the cause for the previous problem.
I downloaded -source.zip, unzipped it and then compiled.
However, if I digit "bowtie2", I have this message "command not found".
What's the problem? what I have to do to add bowtie2 to PATH without damage in my system ?
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Old 08-04-2014, 12:32 PM   #26
dpryan
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You just need to do what Genomax and I mentioned.

BTW, you would do well to buy a book on using Linux (or Unix or even Mac OS X from the command line). This sort of thing should be covered in such a book.
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Old 08-05-2014, 01:29 AM   #27
simobioinfo
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Thank you again for your help. I solved my problems with shell and also to add bowtie to PATH.
Bye
Simona
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Old 09-22-2014, 11:48 AM   #28
zillur
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Default Bow-tie

Hey Guys,
I am new here. I have a problem to run bow tie on my mac. Here is my command line on terminal: Mds-MacBook-Pro:bioinformatics ZILLURRAHMAN$ cd bow-tie
Mds-MacBook-Pro:bow-tie ZILLURRAHMAN$ ls
2012_Lab_Exercise_2.doc
CGRL - Installing and Using Bowtie.webarchive
How to install Bowtie - SEQanswers.webarchive
Installation and use of Bowtie | Bioinformatics at Viikki campus.webarchive
Trinity (runs local) | Applied Bioinformatics Journal Club.webarchive
bowtie2-2.2.3
ernestturro_mappingpractical.pdf
Mds-MacBook-Pro:bow-tie ZILLURRAHMAN$ cd bowtie2-2.2.3
Mds-MacBook-Pro:bowtie2-2.2.3 ZILLURRAHMAN$ make

Then it showed an error message like this:

Agreeing to the Xcode/iOS license requires admin privileges, please re-run as root via sudo.


What should I do now?
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Old 09-22-2014, 01:56 PM   #29
GenoMax
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I assume you have the latest Xcode installed. Try running the make as follows.
Code:
$ sudo make
As an aside, please avoid using spaces in names with OS X. Replace the spaces with an "_" when you need a delimiter.
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Old 09-22-2014, 04:16 PM   #30
zillur
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Thank you very much. With this command the terminal showing this message:
Mds-MacBook-Pro:bowtie2-2.2.3 ZILLURRAHMAN$ sudo make
make: *** No targets specified and no makefile found. Stop.

what should I do now?
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Old 09-22-2014, 11:37 PM   #31
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It appears that you must have downloaded the pre-compiled binary for OS X. In that case you do not need to "make"/compile the program. You should be able to run it directly (may need to add execute permissions to bowtie2 binary).

If you are new to command line/would like to pickup some basics of unix from this excellent resource: http://korflab.ucdavis.edu/Unix_and_...ent.html#part1
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Old 09-23-2014, 12:42 PM   #32
zillur
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Thank you very much. Now I am learning some basic command lines.
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Old 09-26-2014, 07:49 AM   #33
zillur
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Here is my files. When I started with the bowtie command terminal is showing the following result. What should I do now?
Mds-MacBook-Pro:~ ZILLURRAHMAN$ cd bowtie2-2.2.3
Mds-MacBook-Pro:bowtie2-2.2.3 ZILLURRAHMAN$ ls
AUTHORS bowtie2-align-l-debug bowtie2-inspect-l
LICENSE bowtie2-align-s bowtie2-inspect-l-debug
MANUAL bowtie2-align-s-debug bowtie2-inspect-s
MANUAL.markdown bowtie2-build bowtie2-inspect-s-debug
NEWS bowtie2-build-l doc
TUTORIAL bowtie2-build-l-debug example
VERSION bowtie2-build-s scripts
bowtie2 bowtie2-build-s-debug
bowtie2-align-l bowtie2-inspect
Mds-MacBook-Pro:bowtie2-2.2.3 ZILLURRAHMAN$ ./bowtie -a -v 2 e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT
-bash: ./bowtie: No such file or directory
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Old 09-26-2014, 07:58 AM   #34
GenoMax
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Quote:
Originally Posted by zillur View Post
bowtie2
Mds-MacBook-Pro:bowtie2-2.2.3 ZILLURRAHMAN$ ./bowtie -a -v 2 e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT
-bash: ./bowtie: No such file or directory
The name of the program is bowtie2 so you should run

Code:
$ ./bowtie2 -a -v 2 e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT
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Old 09-26-2014, 08:08 AM   #35
zillur
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Thank you very much. I have type the followings but.......

Mds-MacBook-Pro:~ ZILLURRAHMAN$ ./bowtie2 -a -v 2 e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT
-bash: ./bowtie2: No such file or directory
Mds-MacBook-Pro:~ ZILLURRAHMAN$ ./bowtie2-2.2.3 -a -v 2 e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT
-bash: ./bowtie2-2.2.3: is a directory
Mds-MacBook-Pro:~ ZILLURRAHMAN$ ./bowtie2 -a -v 2 e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT
-bash: ./bowtie2: No such file or directory
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Old 09-26-2014, 08:10 AM   #36
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Can you provide a long listing
Code:
$ ls -l
of the directory? I thought your post above had the right file listed.
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Old 09-26-2014, 08:13 AM   #37
zillur
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Ya sure.

Mds-MacBook-Pro:~ ZILLURRAHMAN$ ls -l
total 4688
drwx------ 5 ZILLURRAHMAN staff 170 Sep 25 19:52 Applications
drwx------+ 9 ZILLURRAHMAN staff 306 Sep 19 15:21 Desktop
drwx------+ 12 ZILLURRAHMAN staff 408 Sep 22 15:00 Documents
drwx------+ 224 ZILLURRAHMAN staff 7616 Sep 25 19:25 Downloads
drwx------@ 50 ZILLURRAHMAN staff 1700 Sep 11 11:49 Library
drwx------+ 3 ZILLURRAHMAN staff 102 Aug 27 22:46 Movies
drwx------+ 7 ZILLURRAHMAN staff 238 Sep 3 18:11 Music
drwx------+ 5 ZILLURRAHMAN staff 170 Aug 28 09:57 Pictures
-rw-r--r--@ 1 ZILLURRAHMAN staff 2395395 Sep 3 14:53 PopulusHelp.pdf
drwxr-xr-x+ 6 ZILLURRAHMAN staff 204 Sep 25 19:57 Public
drwxr-xr-x@ 28 ZILLURRAHMAN staff 952 Sep 11 10:28 bowtie2-2.2.3
drwxr-xr-x 2 ZILLURRAHMAN staff 68 Sep 23 00:03 folder
drwxr-xr-x 2 ZILLURRAHMAN staff 68 Sep 23 00:03 new
drwxr-xr-x 3 ZILLURRAHMAN staff 102 Sep 23 00:05 newfolder
-rw-r--r-- 1 ZILLURRAHMAN staff 77 Aug 28 16:56 project.uprj
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Old 09-26-2014, 08:22 AM   #38
zillur
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Is that what you wanted?
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Old 09-26-2014, 08:27 AM   #39
GenoMax
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You are trying to run the program from the current folder which is the wrong folder (did you read about the concept of relative paths at the Korf UNIX site? This is an extremely important concept to learn, when you are new to command line).

Based on your file listing try (from the directory where you provided the long list)

I do not remember if the e_coli data comes with the program. If it is there in the bowtie2 folder then you can omit (/you_need_to_provide_path_to/) part.

Code:
$ bowtie2-2.2.3/bin/bowtie2 -a -v 2 /you_need_to_provide_path_to/e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT
or

Code:
$ cd bowtie2-2.2.3
$ bin/bowtie2 -a -v 2 /you_need_to_provide_path_to/e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT
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Old 09-26-2014, 12:06 PM   #40
zillur
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Thank you very much. Now my bowtie2 is working. Can you give me some beginner tips to build an index. I have this:

mds-macbook-pro:bow-tie ZILLURRAHMAN$ cd bowtie2-2.2.3
mds-macbook-pro:bowtie2-2.2.3 ZILLURRAHMAN$ ls
AUTHORS bowtie2-align-l-debug bowtie2-inspect-l
LICENSE bowtie2-align-s bowtie2-inspect-l-debug
MANUAL bowtie2-align-s-debug bowtie2-inspect-s
MANUAL.markdown bowtie2-build bowtie2-inspect-s-debug
NEWS bowtie2-build-l doc
TUTORIAL bowtie2-build-l-debug example
VERSION bowtie2-build-s scripts
bowtie2 bowtie2-build-s-debug
bowtie2-align-l bowtie2-inspect
mds-macbook-pro:bowtie2-2.2.3 ZILLURRAHMAN$ cd example
mds-macbook-pro:example ZILLURRAHMAN$ ls
index reads reference
mds-macbook-pro:example ZILLURRAHMAN$ cd index
mds-macbook-pro:index ZILLURRAHMAN$ ls
lambda_virus.1.bt2 lambda_virus.3.bt2 lambda_virus.rev.1.bt2
lambda_virus.2.bt2 lambda_virus.4.bt2 lambda_virus.rev.2.bt2
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