Error in running Bowtie2

[Rajeshwarira]

Hello Guy,
I have followed your instructions to install bowtie2 but still I'm not able to use it in RNAlysis.
I'm getting the error mentioned below :

Traceback (most recent call last):

File "rnalysis\utils\io.py", line 1479, in generate_base_call

File "rnalysis\utils\io.py", line 1420, in run_subprocess

File "subprocess.py", line 858, in init

File "subprocess.py", line 1311, in _execute_child

FileNotFoundError: [WinError 2] The system cannot find the file specified

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File "rnalysis\gui\gui.py", line 3697, in finish_generic_job

File "rnalysis\gui\gui_widgets.py", line 329, in run

File "rnalysis\fastq.py", line 747, in bowtie2_align_paired_end

File "rnalysis\fastq.py", line 803, in _parse_bowtie2_misc_args

File "rnalysis\utils\io.py", line 1482, in generate_base_call

FileNotFoundError: RNAlysis could not find 'bowtie2'. Please ensure that your installation folder is correct, or add it to PATH.

I have been trying to figure out this from the past two days. Still I didn't find any solution.

Can you please help me with this?

Thank you
Regards

[Rajeshwarira]

Hello Guy,
Please do help me with this.
I'm really in need of it.
Thank you

[GuyTeichman]

Hi,
What is the value you set for the parameter "bowtie2_installation_folder"?

[Rajeshwarira]

I didn't set any I went with the default.

…

On Thu, May 25, 2023, 4:27 PM Guy Teichman ***@***.***> wrote: Hi, What is the value you set for the parameter "bowtie2_installation_folder"? — Reply to this email directly, view it on GitHub <#23 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A6TURHLUIZL4OL4HVQ3T4O3XH43KBANCNFSM6AAAAAAYM3ZY6M> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[Rajeshwarira]

Hello Guy, Good noon, Can you please guide me what parameters am I suppose to set ?? On Thu, May 25, 2023, 4:54 PM rajarajeshwari rajkumar < ***@***.***> wrote:

…

I didn't set any I went with the default. On Thu, May 25, 2023, 4:27 PM Guy Teichman ***@***.***> wrote: > Hi, > What is the value you set for the parameter "bowtie2_installation_folder"? > > — > Reply to this email directly, view it on GitHub > <#23 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/A6TURHLUIZL4OL4HVQ3T4O3XH43KBANCNFSM6AAAAAAYM3ZY6M> > . > You are receiving this because you authored the thread.Message ID: > ***@***.***> >

[Rajeshwarira]

The parameters now is @echo off perl %~dp0/bowtie2 %* On Fri, May 26, 2023, 12:05 PM rajarajeshwari rajkumar < ***@***.***> wrote:

…

Hello Guy, Good noon, Can you please guide me what parameters am I suppose to set ?? On Thu, May 25, 2023, 4:54 PM rajarajeshwari rajkumar < ***@***.***> wrote: > I didn't set any I went with the default. > > On Thu, May 25, 2023, 4:27 PM Guy Teichman ***@***.***> > wrote: > >> Hi, >> What is the value you set for the parameter >> "bowtie2_installation_folder"? >> >> — >> Reply to this email directly, view it on GitHub >> <#23 (comment)>, >> or unsubscribe >> <https://github.com/notifications/unsubscribe-auth/A6TURHLUIZL4OL4HVQ3T4O3XH43KBANCNFSM6AAAAAAYM3ZY6M> >> . >> You are receiving this because you authored the thread.Message ID: >> ***@***.***> >> >

[GuyTeichman]

Hi,
please try setting the 'bowtie2_installation_folder' to point to the folder in which you installed bowtie2.

[Rajeshwarira]

Hello Guy, I'm really sorry to bother you a lot. But I'm not sure which is installation folder.

…

On Fri, May 26, 2023, 10:21 PM Guy Teichman ***@***.***> wrote: Hi, please try setting the 'bowtie2_installation_folder' to point to the folder in which you installed bowtie2. — Reply to this email directly, view it on GitHub <#23 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A6TURHPGOZITR5L5MIWIBDTXIDNQBANCNFSM6AAAAAAYM3ZY6M> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[Rajeshwarira]

Hello Guy, Can you please guide me with this step by step?? Thank you On Sat, May 27, 2023, 12:54 PM rajarajeshwari rajkumar < ***@***.***> wrote:

…

Hello Guy, I'm really sorry to bother you a lot. But I'm not sure which is installation folder. On Fri, May 26, 2023, 10:21 PM Guy Teichman ***@***.***> wrote: > Hi, > please try setting the 'bowtie2_installation_folder' to point to the > folder in which you installed bowtie2. > > — > Reply to this email directly, view it on GitHub > <#23 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/A6TURHPGOZITR5L5MIWIBDTXIDNQBANCNFSM6AAAAAAYM3ZY6M> > . > You are receiving this because you authored the thread.Message ID: > ***@***.***> >

[GuyTeichman]

You have downloaded and installed the tool 'bowtie2'. You installed it at a specific location on your computer - this is the "installation folder".
You should set the 'bowtie2_installation_folder' parameter in RNAlysis, so it points to the folder in which you installed bowtie2.