Re: [galaxy-dev] all the data files in .loc files needed to download ?
Hi everyone, Thank you very much for your help. I want to download the complete directory of galaxy data through rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/phiX.But It can't work. And then I try to via http://dan.g2.bx.psu.edu/ by http://datacache.g2.bx.psu.edu/ ,I get 502 Bad Gateway. So what happens? How cat I get the data? Is there another way? Help me please. shenwiyn From: Carl Eberhard Date: 2013-02-27 22:28 To: Ross CC: shenwiyn; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] all the data files in .loc files needed to download ? Hello, Ross makes an important point: if this installation is for more than one user, you should install a more complete database system. This page may help with your decisions there: http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=showredirect=Admin%2FConfig%2FPerformance To your first question Is all the data in datacache.g2.bx.psu.edu/indexes needed?, I would say you should only need the data specific to the subject of your analyses and the tools you plan to use. To your second question can all of these needed data be downloaded (via rsync)? - perhaps you can clarify, please? We don't have any restriction on the amount you rsync from there and you're free to download all the data. If a problem or topic isn't covered in that wiki page, this mailing list is a good place to ask questions related to data set up. Thanks, Carl On Wed, Feb 27, 2013 at 5:44 AM, Ross ross.laza...@gmail.com wrote: Hi, shenwiyn I'd also add: Fourth, replace distributed default sqlite with postgresql to your list if it's for any serious use. Sqlite is ok for testing. On Wed, Feb 27, 2013 at 9:37 PM, shenwiyn shenw...@gmail.com wrote: Hello Carl, Thank you very much for your help.I have some thoughts about installing my local galaxy : First,download the latest source of galaxy from https://bitbucket.org/galaxy/galaxy-dist/ ,then install it in my local computer. Second,install dependencies tools mentioned in http://wiki.galaxyproject.org/Admin/Data%20Integration successfully. Third ,install the needed data and configure the .loc files from the following help of wiki page http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup. Finally ,our installation of local galaxy overs and it works in the mass.Is it right ? And I also have some confusions: First ,How large the total needed data is ?Is all the data in datacache.g2.bx.psu.edu/indexes needed ? Second, can all of these needed data be downloaded (via rsync) by the help of http://wiki.galaxyproject.org/Admin/Data%20Integration? These are the most important questions I concerned about now.I am so thankful for some of you advice. Thank you very much. shenwiyn From: Carl Eberhard Date: 2013-02-23 02:42 To: shenwiyn CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] all the data files in .loc files needed to download ? Hello shenwiyn, You may want to have a look at http://wiki.galaxyproject.org/Admin/Data%20Integration which provides more information specific to the indeces/data you'll need and how to install. Along with data management, that page has instructions on how to download (via rsync) the same data we use on our main server. It may be a good starting point. Thanks, Carl On Thu, Feb 21, 2013 at 8:58 PM, shenwiyn shenw...@foxmail.com wrote: Hi Carl Eberhard, Thank you very much for you help.I have another some questions : First, we need to install the needed data,for example sam_fa_indices.loc file of SAM Tools : index AaegL1 /afs/bx.psu.edu/depot/data/genome/AaegL1/sam_index/AaegL1.fa index AgamP3 /afs/bx.psu.edu/depot/data/genome/AgamP3/sam_index/AgamP3.fa index ailMel1 /afs/bx.psu.edu/depot/data/genome/ailMel1/sam_index/ailMel1.fa index anoCar2 /afs/bx.psu.edu/depot/data/genome/anoCar2/sam_index/anoCar2.fa index apiMel2 /afs/bx.psu.edu/depot/data/genome/apiMel2/sam_index/apiMel2.fa index apiMel3 /afs/bx.psu.edu/depot/data/genome/apiMel3/sam_index/apiMel3.fa index aplCal1 /afs/bx.psu.edu/depot/data/genome/aplCal1/sam_index/aplCal1.fa so we need to download AaegL1.fa,AgamP3.fa,ailMel1.fa,anoCar2.fa,apiMel2.fa,apiMel3.fa,and so on ,then install all of this needed datas to /afs/bx.psu.edu/depot/data/genome/aplCal1/sam_index/,is it right? Second, from the needed datas mentioned in the .loc files in http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup ,we need to download too much data,can we get all these data from some website instead of searching them on Iternet one by one? Thanks, shenwiyn From: Carl Eberhard Date: 2013-02-22 01:20 To: shenwiyn Subject: Re: [galaxy-dev] all the data files in .loc files needed to download ? Hello, Yes a local galaxy requires a few steps in order to install the needed data. The following wiki page should help get you started: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Let me know if you need more information, Carl On Tue, Feb
Re: [galaxy-dev] all the data files in .loc files needed to download ?
Hello Carl, Thank you very much for your help.I have some thoughts about installing my local galaxy : First,download the latest source of galaxy from https://bitbucket.org/galaxy/galaxy-dist/ ,then install it in my local computer. Second,install dependencies tools mentioned in http://wiki.galaxyproject.org/Admin/Data%20Integration successfully. Third ,install the needed data and configure the .loc files from the following help of wiki page http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup. Finally ,our installation of local galaxy overs and it works in the mass.Is it right ? And I also have some confusions: First ,How large the total needed data is ?Is all the data in datacache.g2.bx.psu.edu/indexes needed ? Second, can all of these needed data be downloaded (via rsync) by the help of http://wiki.galaxyproject.org/Admin/Data%20Integration? These are the most important questions I concerned about now.I am so thankful for some of you advice. Thank you very much. shenwiyn From: Carl Eberhard Date: 2013-02-23 02:42 To: shenwiyn CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] all the data files in .loc files needed to download ? Hello shenwiyn, You may want to have a look at http://wiki.galaxyproject.org/Admin/Data%20Integration which provides more information specific to the indeces/data you'll need and how to install. Along with data management, that page has instructions on how to download (via rsync) the same data we use on our main server. It may be a good starting point. Thanks, Carl On Thu, Feb 21, 2013 at 8:58 PM, shenwiyn shenw...@foxmail.com wrote: Hi Carl Eberhard, Thank you very much for you help.I have another some questions : First, we need to install the needed data,for example sam_fa_indices.loc file of SAM Tools : index AaegL1 /afs/bx.psu.edu/depot/data/genome/AaegL1/sam_index/AaegL1.fa index AgamP3 /afs/bx.psu.edu/depot/data/genome/AgamP3/sam_index/AgamP3.fa index ailMel1 /afs/bx.psu.edu/depot/data/genome/ailMel1/sam_index/ailMel1.fa index anoCar2 /afs/bx.psu.edu/depot/data/genome/anoCar2/sam_index/anoCar2.fa index apiMel2 /afs/bx.psu.edu/depot/data/genome/apiMel2/sam_index/apiMel2.fa index apiMel3 /afs/bx.psu.edu/depot/data/genome/apiMel3/sam_index/apiMel3.fa index aplCal1 /afs/bx.psu.edu/depot/data/genome/aplCal1/sam_index/aplCal1.fa so we need to download AaegL1.fa,AgamP3.fa,ailMel1.fa,anoCar2.fa,apiMel2.fa,apiMel3.fa,and so on ,then install all of this needed datas to /afs/bx.psu.edu/depot/data/genome/aplCal1/sam_index/,is it right? Second, from the needed datas mentioned in the .loc files in http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup ,we need to download too much data,can we get all these data from some website instead of searching them on Iternet one by one? Thanks, shenwiyn From: Carl Eberhard Date: 2013-02-22 01:20 To: shenwiyn Subject: Re: [galaxy-dev] all the data files in .loc files needed to download ? Hello, Yes a local galaxy requires a few steps in order to install the needed data. The following wiki page should help get you started: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Let me know if you need more information, Carl On Tue, Feb 19, 2013 at 3:59 AM, shenwiyn shenw...@gmail.com wrote: Hi all, Are all the data files in .loc files needed to download and put to the right directory when we install our local galaxy? thaks shenwiyn shenwiyn ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] all the data files in .loc files needed to download ?
Hi, shenwiyn I'd also add: Fourth, replace distributed default sqlite with postgresql to your list if it's for any serious use. Sqlite is ok for testing. On Wed, Feb 27, 2013 at 9:37 PM, shenwiyn shenw...@gmail.com wrote: ** **Hello Carl, Thank you very much for your help.I have some thoughts about installing my local galaxy : First,download the latest source of galaxy from https://bitbucket.org/galaxy/galaxy-dist/ ,then install it in my local computer. Second,install dependencies tools mentioned in http://wiki.galaxyproject.org/Admin/Data%20Integration successfully. Third ,install the needed data and configure the .loc files from the following help of wiki page http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup. Finally ,our installation of local galaxy overs and it works in the mass.Is it right ? And I also have some confusions: First ,How large the total needed data is ?Is all the data in datacache.g2.bx.psu.edu/indexes needed ? Second, can all of these needed data be downloaded (via rsync) by the help of http://wiki.galaxyproject.org/Admin/Data%20Integration? These are the most important questions I concerned about now.I am so thankful for some of you advice. Thank you very much. -- shenwiyn *From:* Carl Eberhard carlfeberh...@gmail.com *Date:* 2013-02-23 02:42 *To:* shenwiyn shenw...@foxmail.com *CC:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] all the data files in .loc files needed to download ? Hello shenwiyn, You may want to have a look at http://wiki.galaxyproject.org/Admin/Data%20Integration which provides more information specific to the indeces/data you'll need and how to install. Along with data management, that page has instructions on how to download (via rsync) the same data we use on our main server. It may be a good starting point. Thanks, Carl On Thu, Feb 21, 2013 at 8:58 PM, shenwiyn shenw...@foxmail.com wrote: ** Hi Carl Eberhard, Thank you very much for you help.I have another some questions : First, we need to install the needed data,for example sam_fa_indices.loc file of SAM Tools : index AaegL1 /afs/bx.psu.edu/depot/data/genome/AaegL1/sam_index/AaegL1 .fa index AgamP3 /afs/bx.psu.edu/depot/data/genome/AgamP3/sam_index/AgamP3 .fa index ailMel1 /afs/bx.psu.edu/depot/data/genome/ailMel1/sam_index/ ailMel1.fa index anoCar2 /afs/bx.psu.edu/depot/data/genome/anoCar2/sam_index/ anoCar2.fa index apiMel2 /afs/bx.psu.edu/depot/data/genome/apiMel2/sam_index/ apiMel2.fa index apiMel3 /afs/bx.psu.edu/depot/data/genome/apiMel3/sam_index/ apiMel3.fa index aplCal1 /afs/bx.psu.edu/depot/data/genome/aplCal1/sam_index/ aplCal1.fa so we need to download AaegL1.fa,AgamP3.fa,ailMel1.fa,anoCar2.fa,apiMel2. fa,apiMel3.fa,and so on ,then install all of this needed datas to /afs/bx .psu.edu/depot/data/genome/aplCal1/sam_index/,is it right? Second, from the needed datas mentioned in the .loc files in http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup ,we need to download too much data,can we get all these data from some website instead of searching them on Iternet one by one? Thanks, shenwiyn -- *From:* Carl Eberhard carlfeberh...@gmail.com *Date:* 2013-02-22 01:20 *To:* shenwiyn shenw...@gmail.com *Subject:* Re: [galaxy-dev] all the data files in .loc files needed to download ? Hello, Yes a local galaxy requires a few steps in order to install the needed data. The following wiki page should help get you started: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Let me know if you need more information, Carl On Tue, Feb 19, 2013 at 3:59 AM, shenwiyn shenw...@gmail.com wrote: ** Hi all, Are all the data files in .loc files needed to download and put to the right directory when we install our local galaxy? thaks shenwiyn -- ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] all the data files in .loc files needed to download ?
Hello, Ross makes an important point: if this installation is for more than one user, you should install a more complete database system. This page may help with your decisions there: http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=showredirect=Admin%2FConfig%2FPerformance To your first question Is all the data in datacache.g2.bx.psu.edu/indexes needed?, I would say you should only need the data specific to the subject of your analyses and the tools you plan to use. To your second question can all of these needed data be downloaded (via rsync)? - perhaps you can clarify, please? We don't have any restriction on the amount you rsync from there and you're free to download all the data. If a problem or topic isn't covered in that wiki page, this mailing list is a good place to ask questions related to data set up. Thanks, Carl On Wed, Feb 27, 2013 at 5:44 AM, Ross ross.laza...@gmail.com wrote: Hi, shenwiyn I'd also add: Fourth, replace distributed default sqlite with postgresql to your list if it's for any serious use. Sqlite is ok for testing. On Wed, Feb 27, 2013 at 9:37 PM, shenwiyn shenw...@gmail.com wrote: ** **Hello Carl, Thank you very much for your help.I have some thoughts about installing my local galaxy : First,download the latest source of galaxy from https://bitbucket.org/galaxy/galaxy-dist/ ,then install it in my local computer. Second,install dependencies tools mentioned in http://wiki.galaxyproject.org/Admin/Data%20Integration successfully. Third ,install the needed data and configure the .loc files from the following help of wiki page http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup. Finally ,our installation of local galaxy overs and it works in the mass.Is it right ? And I also have some confusions: First ,How large the total needed data is ?Is all the data in datacache.g2.bx.psu.edu/indexes needed ? Second, can all of these needed data be downloaded (via rsync) by the help of http://wiki.galaxyproject.org/Admin/Data%20Integration? These are the most important questions I concerned about now.I am so thankful for some of you advice. Thank you very much. -- shenwiyn *From:* Carl Eberhard carlfeberh...@gmail.com *Date:* 2013-02-23 02:42 *To:* shenwiyn shenw...@foxmail.com *CC:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] all the data files in .loc files needed to download ? Hello shenwiyn, You may want to have a look at http://wiki.galaxyproject.org/Admin/Data%20Integration which provides more information specific to the indeces/data you'll need and how to install. Along with data management, that page has instructions on how to download (via rsync) the same data we use on our main server. It may be a good starting point. Thanks, Carl On Thu, Feb 21, 2013 at 8:58 PM, shenwiyn shenw...@foxmail.com wrote: ** Hi Carl Eberhard, Thank you very much for you help.I have another some questions : First, we need to install the needed data,for example sam_fa_indices.loc file of SAM Tools : index AaegL1 /afs/bx.psu.edu/depot/data/genome/AaegL1/sam_index/ AaegL1.fa index AgamP3 /afs/bx.psu.edu/depot/data/genome/AgamP3/sam_index/ AgamP3.fa index ailMel1 /afs/bx.psu.edu/depot/data/genome/ailMel1/sam_index/ ailMel1.fa index anoCar2 /afs/bx.psu.edu/depot/data/genome/anoCar2/sam_index/ anoCar2.fa index apiMel2 /afs/bx.psu.edu/depot/data/genome/apiMel2/sam_index/ apiMel2.fa index apiMel3 /afs/bx.psu.edu/depot/data/genome/apiMel3/sam_index/ apiMel3.fa index aplCal1 /afs/bx.psu.edu/depot/data/genome/aplCal1/sam_index/ aplCal1.fa so we need to download AaegL1.fa,AgamP3.fa,ailMel1.fa,anoCar2.fa,apiMel2 .fa,apiMel3.fa,and so on ,then install all of this needed datas to /afs/ bx.psu.edu/depot/data/genome/aplCal1/sam_index/,is it right? Second, from the needed datas mentioned in the .loc files in http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup ,we need to download too much data,can we get all these data from some website instead of searching them on Iternet one by one? Thanks, shenwiyn -- *From:* Carl Eberhard carlfeberh...@gmail.com *Date:* 2013-02-22 01:20 *To:* shenwiyn shenw...@gmail.com *Subject:* Re: [galaxy-dev] all the data files in .loc files needed to download ? Hello, Yes a local galaxy requires a few steps in order to install the needed data. The following wiki page should help get you started: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Let me know if you need more information, Carl On Tue, Feb 19, 2013 at 3:59 AM, shenwiyn shenw...@gmail.com wrote: ** Hi all, Are all the data files in .loc files needed to download and put to the right directory when we install our local galaxy? thaks shenwiyn -- ___ Please keep all replies on the
Re: [galaxy-dev] all the data files in .loc files needed to download ?
Hello shenwiyn, You may want to have a look at http://wiki.galaxyproject.org/Admin/Data%20Integration which provides more information specific to the indeces/data you'll need and how to install. Along with data management, that page has instructions on how to download (via rsync) the same data we use on our main server. It may be a good starting point. Thanks, Carl On Thu, Feb 21, 2013 at 8:58 PM, shenwiyn shenw...@foxmail.com wrote: ** Hi Carl Eberhard, Thank you very much for you help.I have another some questions : First, we need to install the needed data,for example sam_fa_indices.loc file of SAM Tools : index AaegL1 /afs/bx.psu.edu/depot/data/genome/AaegL1/sam_index/AaegL1. fa index AgamP3 /afs/bx.psu.edu/depot/data/genome/AgamP3/sam_index/AgamP3. fa index ailMel1 /afs/bx.psu.edu/depot/data/genome/ailMel1/sam_index/ ailMel1.fa index anoCar2 /afs/bx.psu.edu/depot/data/genome/anoCar2/sam_index/ anoCar2.fa index apiMel2 /afs/bx.psu.edu/depot/data/genome/apiMel2/sam_index/ apiMel2.fa index apiMel3 /afs/bx.psu.edu/depot/data/genome/apiMel3/sam_index/ apiMel3.fa index aplCal1 /afs/bx.psu.edu/depot/data/genome/aplCal1/sam_index/ aplCal1.fa so we need to download AaegL1.fa,AgamP3.fa,ailMel1.fa,anoCar2.fa,apiMel2. fa,apiMel3.fa,and so on ,then install all of this needed datas to /afs/bx. psu.edu/depot/data/genome/aplCal1/sam_index/,is it right? Second, from the needed datas mentioned in the .loc files in http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup ,we need to download too much data,can we get all these data from some website instead of searching them on Iternet one by one? Thanks, shenwiyn -- *From:* Carl Eberhard carlfeberh...@gmail.com *Date:* 2013-02-22 01:20 *To:* shenwiyn shenw...@gmail.com *Subject:* Re: [galaxy-dev] all the data files in .loc files needed to download ? Hello, Yes a local galaxy requires a few steps in order to install the needed data. The following wiki page should help get you started: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Let me know if you need more information, Carl On Tue, Feb 19, 2013 at 3:59 AM, shenwiyn shenw...@gmail.com wrote: ** Hi all, Are all the data files in .loc files needed to download and put to the right directory when we install our local galaxy? thaks shenwiyn -- shenwiyn ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
