temporary files should go to specifically folder.

[yujun2017]

Tbprofiler will be failed if we ran it in tomcat. we do find there is a bug in TBProfiler and we already fixed the bug and want to know if we can upload changed file.

[jodyphelan]

Hi @yujun2017, thanks for looking into fixing the issue. Do you have a fork of the repo you can create a pull request from?

[yujun2017]

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[jodyphelan]

What you should do is to:

1. Fork the repository. I see you have a fork already but it is quite an old version.
2. Make the changes and commit
3. Create a pull request. More info here

[yujun2017]

Jody: I just created a new pull request and I can't find way to upload files. Github is little bit new for me to make file changing. I do one time long time ago in tb-profiler. I just forgot it. I can send file to you and you can review and merge file if you think it is ok. Thanks! John

…

On Thu, 2 Jan 2020 at 05:48, Jody Phelan ***@***.***> wrote: What you should do is to: 1. Fork the repository. I see you have a fork already but it is quite an old version. 2. Make the changes and commit 3. Create a pull request. More info here <https://help.github.com/en/github/collaborating-with-issues-and-pull-requests/creating-a-pull-request> — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#78?email_source=notifications&email_token=AGDIGTDHWJXTA24FUK7Z64TQ3XA7NA5CNFSM4KBM73S2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEH6CQAY#issuecomment-570173443>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGDIGTCR7CEIQCLSRVKNZ3DQ3XA7NANCNFSM4KBM73SQ> .

-- John Yu

[jodyphelan]

Hi John,

Sure! You can upload to gist and share the url. If you could put in some comments where you have made changes that would be great!

Jody

[yujun2017]

Jodt: I have created a pull request in my account. you can merge it into your branch. Here is what i have changed. After this changing, the file name will become to (prefix)*C**hromosome_xxxx_xxxx.vcf.gz. *the filename will be unique and the file will go to special folder. if bed_file: self.windows_cmd = "cat %(bed_file)s | awk '{print $1\":\"$2\"-\"$3\" *%(prefix)s*\"$1\"_\"$2\"_\"$3}'" % vars(self) else: self.windows_cmd = "bedtools makewindows -g %(ref_file)s.fai -n %(threads)s | awk '{print $1\":\"$2+1\"-\"$3\" *%(prefix)s*\"$1\"_\"$2+1\"_\"$3}'" % vars(self) Thanks! John

…

On Thu, 2 Jan 2020 at 18:26, Jody Phelan ***@***.***> wrote: Hi John, Sure! You can upload to gist <https://gist.github.com/> and share the url. If you could put in some comments where you have made changes that would be great! Jodt — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#78?email_source=notifications&email_token=AGDIGTDDBKU5IE5IZHDKBQ3Q3ZZ3BA5CNFSM4KBM73S2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEH7ZDHI#issuecomment-570397085>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGDIGTFS73XIFVKUARGZZ3DQ3ZZ3BANCNFSM4KBM73SQ> .

-- John Yu

[jodyphelan]

Hi John,

At the moment the code from your fork seems to fail.
Do you want the VCF files to be made in the directory set with -d? If so this is already fixed in the latest version see f86bdda.

The current code will append %(prefix)s during the bcftools call command as below:

self.calling_cmd = "bcftools mpileup -f %(ref_file)s -Bq8 -a DP,AD -r {1} %(bam_file)s | bcftools call -mv | bcftools filter -e 'FMT/DP<10' | bcftools filter -e 'IMF < 0.7' -s 0 -Oz -o %(prefix)s.{2}.vcf.gz" % vars(self)

If we also it %(prefix)s into the self.windows_cmd variable it will try to save the VCFs to a folder which does not exist. For example if we set -d /save_dir then it will try to create the VCF:

/save_dir/save_dir/Chromosome_XX_YY.vcf.gz

Have you tested tomcat with tb-profiler v2.8?

Thanks for looking into it!

[jodyphelan]

Are installing via conda? I noticed that it isn't updated with this patch yet!

[yujun2017]

Yes. we are using conda to install it. I will re-test latest code. When i got v2.8, it has same issue. We have to think about multi-user case. the Chromosome_XX_YY.vcf.gz must be unique, otherwise these files will be overwrite by anouther tbprofiler call. this is why I add save_dir into file name. the file will not go to new folder. the filename will be: *xxxx*Chromosome_XX_YY.vcf.gz (xxxx is unique for my case). John

…

On Fri, 3 Jan 2020 at 11:39, Jody Phelan ***@***.***> wrote: Are installing via conda? I noticed that it isn't updated with this patch yet! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#78?email_source=notifications&email_token=AGDIGTEDELXWIAW7ML66TPTQ35S57A5CNFSM4KBM73S2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEIBRCUI#issuecomment-570626385>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGDIGTAWM47NOEENWY2ZEBLQ35S57ANCNFSM4KBM73SQ> .

-- John Yu

[jodyphelan]

Ah ok, this should be fixed in the latest commit on github but not on conda yet. I'll update the conda recipe and let you know when it is finished.

[yujun2017]

great. Thank you so much! John

…

On Fri, 3 Jan 2020 at 11:50, Jody Phelan ***@***.***> wrote: Ah ok, this should be fixed in the latest commit on github but not on conda yet. I'll update the conda recipe and let you know when it is finished. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#78?email_source=notifications&email_token=AGDIGTGZ5QNZ4PQVESWRUOTQ35UEJA5CNFSM4KBM73S2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEIBR2OQ#issuecomment-570629434>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGDIGTGQ5ZUJGDVZTZVICITQ35UEJANCNFSM4KBM73SQ> .

-- John Yu

[jodyphelan]

It should be released on conda now. Please check and let me konw if it works ok.

[yujun2017]

I will test it next Monday and will let you know. John

…

Sent from my iPhone

On Jan 3, 2020, at 8:14 PM, Jody Phelan ***@***.***> wrote:  It should be released on conda now. Please check and let me konw if it works ok. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

[yujun2017]

I just got latest code and it works fine now. Thank you very much! John

…

On Fri, 3 Jan 2020 at 22:35, John Yu ***@***.***> wrote: I will test it next Monday and will let you know. John Sent from my iPhone On Jan 3, 2020, at 8:14 PM, Jody Phelan ***@***.***> wrote:  It should be released on conda now. Please check and let me konw if it works ok. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

-- John Yu

[jodyphelan]

Perfect!