Running own data example

Jokendo-collab commented 4 years ago

Count you give an example on how one can run his/her own data using this wonderful pipeline. This information is lacking in the tutorial section

wenbostar commented 4 years ago

We have some examples in this tutorial: http://bioconductor.org/packages/devel/bioc/vignettes/PGA/inst/doc/PGA.pdf.

Jokendo-collab commented 4 years ago

Hi,

What is causing this error: Error in system(command = tandemparser, intern = TRUE) : 'C:\Program' not found

Kindly help

On Sun, May 3, 2020 at 11:36 PM Bo notifications@github.com wrote:

We have some examples in this tutorial: http://bioconductor.org/packages/devel/bioc/vignettes/PGA/inst/doc/PGA.pdf .

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wenbostar commented 4 years ago

Could you please install the version at github by using the following code? Please let me know if you still get this error using the new version.

BiocManager::install("wenbostar/PGA")

Jokendo-collab commented 4 years ago

Hi,

The error is still there after using

BiocManager::install("wenbostar/PGA")

to install the package.

On Tue, May 5, 2020 at 7:20 PM Bo notifications@github.com wrote:

Could you please install the version at github by using the following code? Please let me know if you still get this error using the new version.

BiocManager::install("wenbostar/PGA")

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/wenbostar/PGA/issues/14#issuecomment-624192662, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGJ34O35IDWKQAYHB4CVTQ3RQBDEFANCNFSM4MYJEPFA .

wenbostar commented 4 years ago

Could you please send me the code so that I can reproduce the error for debugging?

Jokendo-collab commented 4 years ago

I meant that the following error is still coming up Error in system(command = tandemparser, intern = TRUE) : 'C:\Program' not found

On Tue, May 5, 2020 at 10:17 PM Javan Okendo javanokendo@gmail.com wrote:

Hi,

The error is still there after using

BiocManager::install("wenbostar/PGA")

to install the package.

On Tue, May 5, 2020 at 7:20 PM Bo notifications@github.com wrote:

Could you please install the version at github by using the following code? Please let me know if you still get this error using the new version.

BiocManager::install("wenbostar/PGA")

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/wenbostar/PGA/issues/14#issuecomment-624192662, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGJ34O35IDWKQAYHB4CVTQ3RQBDEFANCNFSM4MYJEPFA .

Jokendo-collab commented 4 years ago

Hi,

Here is the code:parserGear(file = idfile, db = dbfile, decoyPrefix="#REV#",xmx=1,thread=8,outdir = "parser_outdir")

On Tue, May 5, 2020 at 10:20 PM Javan Okendo javanokendo@gmail.com wrote:

I meant that the following error is still coming up Error in system(command = tandemparser, intern = TRUE) : 'C:\Program' not found

On Tue, May 5, 2020 at 10:17 PM Javan Okendo javanokendo@gmail.com wrote:

Hi,

The error is still there after using

BiocManager::install("wenbostar/PGA")

to install the package.

On Tue, May 5, 2020 at 7:20 PM Bo notifications@github.com wrote:

Could you please install the version at github by using the following code? Please let me know if you still get this error using the new version.

BiocManager::install("wenbostar/PGA")

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/wenbostar/PGA/issues/14#issuecomment-624192662, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGJ34O35IDWKQAYHB4CVTQ3RQBDEFANCNFSM4MYJEPFA .

wenbostar / PGA

Running own data example #14