Running own data example

[Jokendo-collab]

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]

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

[Jokendo-collab]

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

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On Sun, May 3, 2020 at 11:36 PM Bo ***@***.***> wrote: We have some examples in this tutorial: http://bioconductor.org/packages/devel/bioc/vignettes/PGA/inst/doc/PGA.pdf . — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#14 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGJ34OYCNTPXX6XC3SNV773RPXPVNANCNFSM4MYJEPFA> .

[wenbostar]

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]

Hi, The error is still there after using BiocManager::install("wenbostar/PGA") to install the package.

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On Tue, May 5, 2020 at 7:20 PM Bo ***@***.***> 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 <#14 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGJ34O35IDWKQAYHB4CVTQ3RQBDEFANCNFSM4MYJEPFA> .

[wenbostar]

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

[Jokendo-collab]

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

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On Tue, May 5, 2020 at 10:17 PM Javan Okendo ***@***.***> 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 ***@***.***> 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 > <#14 (comment)>, or > unsubscribe > <https://github.com/notifications/unsubscribe-auth/AGJ34O35IDWKQAYHB4CVTQ3RQBDEFANCNFSM4MYJEPFA> > . >

[Jokendo-collab]

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

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On Tue, May 5, 2020 at 10:20 PM Javan Okendo ***@***.***> 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 ***@***.***> 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 ***@***.***> 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 >> <#14 (comment)>, or >> unsubscribe >> <https://github.com/notifications/unsubscribe-auth/AGJ34O35IDWKQAYHB4CVTQ3RQBDEFANCNFSM4MYJEPFA> >> . >> >