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glennhickey / progressiveCactus

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules
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starting troubles... #33

Open GGopinath opened 9 years ago

GGopinath commented 9 years ago

hi, glenn, i think when i started again, the installation got completed. I changed the sed command to: sed -i 's/git:/https:/g' .gitmodules as 'git' is in the file name too and it owuld cause a mess.

I am posting this to the website as you suggested.

Also, i am trying to do a test run with three fasta files on my network drive.i formatted the file name input file as suggested. but i get this error: Unable to write to hal: /home/Gopal.Gopinathrao/progressiveCactus/a specified directory

Temporary data was left in ..(a specified directory)

Is there a troubleshooting guide? under what conditions the script would not do the alignment? the input index file is like this: csak /mnt/Cyclo/10crono/csak894.fasta ctur /mnt/Cyclo/10crono/ctur3032.fasta ccon /mnt/Cyclo/10crono/ccon1330.fasta

the name is a unique string in the header of each contig in the respective files...

thanks and apologies for the bother, ..gopal

From: Glenn Hickey [glenn.hickey@gmail.com] Sent: Wednesday, February 04, 2015 6:17 PM To: Gopinathrao, Gopal Subject: Re: git hub issues Maybe start from scratch: rm -rf progressiveCactus git clone https://github.com/glennhickey/progressiveCactus.git cd progressiveCactus cp .gitmodules .gitmodules.bak sed -e "s/git/https/g" .gitmodules.bak > .gitmodules git submodule update --init make Whether or not that works, can you please continue this conversation (you can copy this thread into your message) via the "issues" link on the webpage? That will get your messages emailed to other developers who may have run into this before.. .

On Wed, Feb 4, 2015 at 6:04 PM, Gopinathrao, Gopal Gopal.GOPINATHRAO@fda.hhs.gov wrote:

hi Glenn,

thanks. i did the replace and many of the submodules got 'registered'wihtout any scripts in them. But the call failed as "Unable to find current revision in submodule path 'submodules/cactus'".

i looked up the cactus repo of Benedict on github. the link is on.

am i supposed to expect the submodules have their constituent set of scripts pulled when i run the --init call?is there a need for updating cactus repo on github?

sorry for the bother and naive questions.

thanks,
..gopal
From: Glenn Hickey [glenn.hickey@gmail.com]
Sent: Wednesday, February 04, 2015 5:48 PM

To: Gopinathrao, Gopal
Subject: Re: git hub issues
Yeah, looks like the same network problem for the submodules.  You can try a similar workaround, which would be to replace occurrences of git:// with https:// in progressiveCactus/.gitmodules *before* running git submodule update --init
make
On Wed, Feb 4, 2015 at 5:40 PM, Gopinathrao, Gopal <Gopal.GOPINATHRAO@fda.hhs.gov> wrote:

    Hi, Glenn,

    thanks for the quick reply.

    Your correction helped. I get the error message when I tried to update teh submodules as per the instructions at this stage:

    Submodule 'submodules/zlib' () registered for path 'submodules/zlib'
    fatal: unable to connect to github.com:
    github.com[0: 192.30.252.129]: errno=Connection timed out

    Unable to fetch in submodule path 'submodules/cactus'

    When I tried to call make at this point, i get the following message:
    Submodule 'submodules/zlib' () registered for path 'submodules/zlib'
    fatal: unable to connect to github.com:
    github.com[0: 192.30.252.129]: errno=Connection timed out

    Unable to fetch in submodule path 'submodules/cactus'

    is it something in the submodules/cactus on git that is causing problem?

    thanks again,
    ..gopal
    From: Glenn Hickey [glenn.hickey@gmail.com]
    Sent: Wednesday, February 04, 2015 5:18 PM
    To: Gopinathrao, Gopal
    Subject: Re: git hub issues
    Hi Gopal,
    I'd never even noticed that GitHub added a "Download as Zip" link.  It doesn't seem to include submodules, however, so I don't think it will help you.  
    You can try using 
    https://github.com/glennhickey/progressiveCactus.git
    instead of 
    git://github.com/glennhickey/progressiveCactus.git
    when following the installation instructions.  
    -Glenn
    On Wed, Feb 4, 2015 at 5:08 PM, Gopinathrao, Gopal <Gopal.GOPINATHRAO@fda.hhs.gov> wrote:

        Hi, Glenn,

        I am writing from US FDA. I am trying to install progressiveCactus from the git link but i get error message about connecting to gib.

        So i downloaded the zip file and copied the pCactus folder.  How to install the software if I am not able to connect to git due to our federal firewall?

        thanks,

        ..gopal

        Gopal R Gopinath, PhD
        Bioinformatician / Biologist
GGopinath commented 9 years ago

I have moved further in running the alignment. NOw I am processing the hal file using hal2assemblyhub.py

the script is asking for sonlib.bioio module that I cannot find anywhere in the libraries. Can someone point to the location to download this module? thanks, ..gopal

glennhickey commented 9 years ago

I don't think it will make a directory path for your hal output parameter. So maybe "a specified directory" doesn't exist and this is causing your error. (it will create the directory passed as the "workDir" parameter though)

On Wed, Feb 4, 2015 at 7:34 PM, GGopinath notifications@github.com wrote:

hi, glenn, i think when i started again, the installation got completed. I changed the sed command to: sed -i 's/git:/https:/g' .gitmodules as 'git' is in the file name too and it owuld cause a mess.

I am posting this to the website as you suggested.

Also, i am trying to do a test run with three fasta files on my network drive.i formatted the file name input file as suggested. but i get this error: Unable to write to hal: /home/Gopal.Gopinathrao/progressiveCactus/a specified directory

Temporary data was left in ..(a specified directory)

Is there a troubleshooting guide? under what conditions the script would not do the alignment? the input index file is like this: csak /mnt/Cyclo/10crono/csak894.fasta ctur /mnt/Cyclo/10crono/ctur3032.fasta ccon /mnt/Cyclo/10crono/ccon1330.fasta

the name is a unique string in the header of each contig in the respective files...

thanks and apologies for the bother, ..gopal

From: Glenn Hickey [glenn.hickey@gmail.com] Sent: Wednesday, February 04, 2015 6:17 PM To: Gopinathrao, Gopal Subject: Re: git hub issues Maybe start from scratch: rm -rf progressiveCactus git clone https://github.com/glennhickey/progressiveCactus.git cd progressiveCactus cp .gitmodules .gitmodules.bak sed -e "s/git/https/g" .gitmodules.bak > .gitmodules git submodule update --init make Whether or not that works, can you please continue this conversation (you can copy this thread into your message) via the "issues" link on the webpage? That will get your messages emailed to other developers who may have run into this before.. .

On Wed, Feb 4, 2015 at 6:04 PM, Gopinathrao, Gopal Gopal.GOPINATHRAO@fda.hhs.gov wrote:

hi Glenn,

thanks. i did the replace and many of the submodules got 'registered'wihtout any scripts in them. But the call failed as "Unable to find current revision in submodule path 'submodules/cactus'".

i looked up the cactus repo of Benedict on github. the link is on.

am i supposed to expect the submodules have their constituent set of scripts pulled when i run the --init call?is there a need for updating cactus repo on github?

sorry for the bother and naive questions.

thanks, ..gopal From: Glenn Hickey [glenn.hickey@gmail.com] Sent: Wednesday, February 04, 2015 5:48 PM

To: Gopinathrao, Gopal Subject: Re: git hub issues Yeah, looks like the same network problem for the submodules. You can try a similar workaround, which would be to replace occurrences of git:// with https:// in progressiveCactus/.gitmodules before running git submodule update --init make On Wed, Feb 4, 2015 at 5:40 PM, Gopinathrao, Gopal Gopal.GOPINATHRAO@fda.hhs.gov wrote:

Hi, Glenn,

thanks for the quick reply.

Your correction helped. I get the error message when I tried to update teh submodules as per the instructions at this stage:

Submodule 'submodules/zlib' () registered for path 'submodules/zlib'
fatal: unable to connect to github.com:
github.com[0: 192.30.252.129]: errno=Connection timed out

Unable to fetch in submodule path 'submodules/cactus'

When I tried to call make at this point, i get the following message:
Submodule 'submodules/zlib' () registered for path 'submodules/zlib'
fatal: unable to connect to github.com:
github.com[0: 192.30.252.129]: errno=Connection timed out

Unable to fetch in submodule path 'submodules/cactus'

is it something in the submodules/cactus on git that is causing problem?

thanks again,
..gopal
From: Glenn Hickey [glenn.hickey@gmail.com]
Sent: Wednesday, February 04, 2015 5:18 PM
To: Gopinathrao, Gopal
Subject: Re: git hub issues
Hi Gopal,
I'd never even noticed that GitHub added a "Download as Zip" link.  It doesn't seem to include submodules, however, so I don't think it will help you.
You can try using
https://github.com/glennhickey/progressiveCactus.git
instead of
git://github.com/glennhickey/progressiveCactus.git
when following the installation instructions.
-Glenn
On Wed, Feb 4, 2015 at 5:08 PM, Gopinathrao, Gopal <Gopal.GOPINATHRAO@fda.hhs.gov> wrote:

    Hi, Glenn,

    I am writing from US FDA. I am trying to install progressiveCactus from the git link but i get error message about connecting to gib.

    So i downloaded the zip file and copied the pCactus folder.  How to install the software if I am not able to connect to git due to our federal firewall?

    thanks,

    ..gopal

    Gopal R Gopinath, PhD
    Bioinformatician / Biologist

— Reply to this email directly or view it on GitHub https://github.com/glennhickey/progressiveCactus/issues/33.