Re: Flexbar source code?
Hi Johannes, On Wed, Jan 30, 2013 at 09:47:48AM +0100, Johannes Röhr wrote: > ok, the plan sounds reasonable. OK. > Besides these issues, I consider to > include the tbb lib in the source tarball to make it easy for those who > download it for compilation. As far as I understood the tbb could be > dropped by the patch for packaging based on tarball, right? Or would > this complicate the packaging process or be against conventions? We do often find tarballs containing convenience copies of certain libraries. In most cases it is possible to use a configuration option to use this copy or a system library. Debian currently has version 4.0+r233 (package libtbb-dev). If this is the same / a compatible version as you intend to include there should be no problems to expect. In the specific case of flexbar I'm lacking enough knowledge for cmake build system. I would consider the following options (prefered in this ranking): 1. Let cmake check whether libtbb is installed on the system and use this if yes 2. Provide a switch that enables forcing the usage of libtbb installed on the system 3. Patch CMakeLists.txt to ignore the convenience copy and take the system libtbb Options 1. and 2. enable us the packaging without applying extra patches which would simplify things on our side but might possibly put some extra work on your shoulders (which you would not have otherwise when ignoring our packaging attempt.) As I said I have no cmake experience and can not tell how much work this might be but in any case I could ask on some other list (debian-mentors) for the changes that might be needed. So if you would be willing to distribute flexbar source implementing 1. or 2. I could try to work out a patch that does exactly this. If you think 3. should be the way to go this is a fallback option for us. > Thank you a lot for the help! Thanks for your cooperation Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130130091045.gd27...@an3as.eu
Re: Flexbar source code?
Hi Andreas, ok, the plan sounds reasonable. Besides these issues, I consider to include the tbb lib in the source tarball to make it easy for those who download it for compilation. As far as I understood the tbb could be dropped by the patch for packaging based on tarball, right? Or would this complicate the packaging process or be against conventions? Thank you a lot for the help! Best, Johannes On Jan 29, 2013, at 8:29 AM, Andreas Tille wrote: > Hi Johannes, > > thanks again for your very helpful clarification. After reading this I > think it might be the best idea if we try to package flexbar as it is > (including seqan copy) for the experimental branch in Debian which helps > Toni for the moment and once there might be some new seqan library > release we will build flexbar using this new release and move it to main > Debian. I guess for the moment this helps those who need flexbar now > and is technically OK. > > Toni, do you consider it reasonable if we do this together at the Debian > Med Sprint in Kiel? > > Johannes, thanks again for sharing your insight and also for providing > flexbar as free software > > Andreas. > > On Mon, Jan 28, 2013 at 04:09:08PM +0100, Johannes Röhr wrote: >> Hi Andreas, >> >> it is completely clear to me that one should use as many packaged libraries >> as possible. I'm simply not sure if it works with the older SeqAn package >> apart from modifications. I would have to test this first, and for reasons >> of consistency I would then go back to this release also on sourceforge. >> Since I know that a lot changes were introduced in the recent year, >> especially in the align module and the argument parser, this could cause >> problems and I also prefer to rely on the recent implementations. >> >> Therefore, I propose to wait for the next SeqAn package release. I will then >> use it also for the Flexbar version on sourceforge and will try to come >> along without modifications. Since I applied only very slight modifications, >> I am optimistic that it works out and I will discuss it with SeqAn >> developers. I definitely prefer to use an official and unmodified release, >> and see it as an aim for coming versions. Besides from cleaner sources and >> packaging, it would then also become obsolete to adjust new SeqAn libs to >> modifications for inclusion in Flexbar. However, I am not sure how fast a >> new packaged release will be provided. >> >> Best regards >> Johannes > > -- > http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/ba2990d1-7d53-4664-b7d8-4d362fd16...@users.sourceforge.net
Re: Flexbar source code?
On 29/01/13 07:29, Andreas Tille wrote: Hi Johannes, thanks again for your very helpful clarification. After reading this I think it might be the best idea if we try to package flexbar as it is (including seqan copy) for the experimental branch in Debian which helps Toni for the moment and once there might be some new seqan library release we will build flexbar using this new release and move it to main Debian. I guess for the moment this helps those who need flexbar now and is technically OK. Toni, do you consider it reasonable if we do this together at the Debian Med Sprint in Kiel? Hi, Andreas. Yes, that would be great! Thanks for your help with this project. Bye, Tony. Johannes, thanks again for sharing your insight and also for providing flexbar as free software Andreas. On Mon, Jan 28, 2013 at 04:09:08PM +0100, Johannes Röhr wrote: Hi Andreas, it is completely clear to me that one should use as many packaged libraries as possible. I'm simply not sure if it works with the older SeqAn package apart from modifications. I would have to test this first, and for reasons of consistency I would then go back to this release also on sourceforge. Since I know that a lot changes were introduced in the recent year, especially in the align module and the argument parser, this could cause problems and I also prefer to rely on the recent implementations. Therefore, I propose to wait for the next SeqAn package release. I will then use it also for the Flexbar version on sourceforge and will try to come along without modifications. Since I applied only very slight modifications, I am optimistic that it works out and I will discuss it with SeqAn developers. I definitely prefer to use an official and unmodified release, and see it as an aim for coming versions. Besides from cleaner sources and packaging, it would then also become obsolete to adjust new SeqAn libs to modifications for inclusion in Flexbar. However, I am not sure how fast a new packaged release will be provided. Best regards Johannes -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/510792c7.2060...@minke.ukfsn.org
Re: Flexbar source code?
Hi Johannes, thanks again for your very helpful clarification. After reading this I think it might be the best idea if we try to package flexbar as it is (including seqan copy) for the experimental branch in Debian which helps Toni for the moment and once there might be some new seqan library release we will build flexbar using this new release and move it to main Debian. I guess for the moment this helps those who need flexbar now and is technically OK. Toni, do you consider it reasonable if we do this together at the Debian Med Sprint in Kiel? Johannes, thanks again for sharing your insight and also for providing flexbar as free software Andreas. On Mon, Jan 28, 2013 at 04:09:08PM +0100, Johannes Röhr wrote: > Hi Andreas, > > it is completely clear to me that one should use as many packaged libraries > as possible. I'm simply not sure if it works with the older SeqAn package > apart from modifications. I would have to test this first, and for reasons of > consistency I would then go back to this release also on sourceforge. Since I > know that a lot changes were introduced in the recent year, especially in the > align module and the argument parser, this could cause problems and I also > prefer to rely on the recent implementations. > > Therefore, I propose to wait for the next SeqAn package release. I will then > use it also for the Flexbar version on sourceforge and will try to come along > without modifications. Since I applied only very slight modifications, I am > optimistic that it works out and I will discuss it with SeqAn developers. I > definitely prefer to use an official and unmodified release, and see it as an > aim for coming versions. Besides from cleaner sources and packaging, it would > then also become obsolete to adjust new SeqAn libs to modifications for > inclusion in Flexbar. However, I am not sure how fast a new packaged release > will be provided. > > Best regards > Johannes -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130129072954.gb31...@an3as.eu
Re: Flexbar source code?
Hi Andreas, it is completely clear to me that one should use as many packaged libraries as possible. I'm simply not sure if it works with the older SeqAn package apart from modifications. I would have to test this first, and for reasons of consistency I would then go back to this release also on sourceforge. Since I know that a lot changes were introduced in the recent year, especially in the align module and the argument parser, this could cause problems and I also prefer to rely on the recent implementations. Therefore, I propose to wait for the next SeqAn package release. I will then use it also for the Flexbar version on sourceforge and will try to come along without modifications. Since I applied only very slight modifications, I am optimistic that it works out and I will discuss it with SeqAn developers. I definitely prefer to use an official and unmodified release, and see it as an aim for coming versions. Besides from cleaner sources and packaging, it would then also become obsolete to adjust new SeqAn libs to modifications for inclusion in Flexbar. However, I am not sure how fast a new packaged release will be provided. Best regards Johannes On Jan 25, 2013, at 11:08 PM, Andreas Tille wrote: > Hi Johannes, > > many thanks for getting involved. > > On Fri, Jan 25, 2013 at 03:11:23PM +0100, Johannes Röhr wrote: >> Tony asked me to join discussion on Flexbar packaging. I'm not sure if the >> stable SeqAn 1.3.1 package release misses functionality that I rely on, or >> if the behaviour of functions changed even if it compiles with this release. >> For example the new ArgumentParser has been added rather recently and I >> would not be surprised if its functionality changed in the time between the >> SeqAn package release and the revision that I incorporated. >> >> However, I think the question is not only if it compiles somehow using this >> package. It should be exacly the same behaviour for one version of Flexbar. >> This isn't clear if the seqan sources differ in version, not to talk about >> slight modifications I made. > > Thanks for the clarifications. I'd take this for some veto to not use > the Debian packaged seqan library. The question is whether the > modifications you made might be incorporated into upstream seqan. If > this would be feasible we could package a seqan version that would fit > flexbar (and most probably other applications.) Do you think this is > possible? > >> Thank you for the interest to include Flexbar! > > Sure. We try to fit the needs of all bioinformatics tasks. > > Kind regards and thanks again for joining here > >Andreas. > > -- > http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/e1de0773-19d4-48db-ad6a-e66e83a39...@users.sourceforge.net
Re: Flexbar source code?
Hi Johannes, many thanks for getting involved. On Fri, Jan 25, 2013 at 03:11:23PM +0100, Johannes Röhr wrote: > Tony asked me to join discussion on Flexbar packaging. I'm not sure if the > stable SeqAn 1.3.1 package release misses functionality that I rely on, or if > the behaviour of functions changed even if it compiles with this release. For > example the new ArgumentParser has been added rather recently and I would not > be surprised if its functionality changed in the time between the SeqAn > package release and the revision that I incorporated. > > However, I think the question is not only if it compiles somehow using this > package. It should be exacly the same behaviour for one version of Flexbar. > This isn't clear if the seqan sources differ in version, not to talk about > slight modifications I made. Thanks for the clarifications. I'd take this for some veto to not use the Debian packaged seqan library. The question is whether the modifications you made might be incorporated into upstream seqan. If this would be feasible we could package a seqan version that would fit flexbar (and most probably other applications.) Do you think this is possible? > Thank you for the interest to include Flexbar! Sure. We try to fit the needs of all bioinformatics tasks. Kind regards and thanks again for joining here Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130125220803.gb12...@an3as.eu
Re: Re: Flexbar source code?
Hi Andreas, Tony asked me to join discussion on Flexbar packaging. I'm not sure if the stable SeqAn 1.3.1 package release misses functionality that I rely on, or if the behaviour of functions changed even if it compiles with this release. For example the new ArgumentParser has been added rather recently and I would not be surprised if its functionality changed in the time between the SeqAn package release and the revision that I incorporated. However, I think the question is not only if it compiles somehow using this package. It should be exacly the same behaviour for one version of Flexbar. This isn't clear if the seqan sources differ in version, not to talk about slight modifications I made. Thank you for the interest to include Flexbar! Best regards Johannes -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/dbd338be-b4f1-4c7b-896c-c3032d981...@users.sourceforge.net
Re: Flexbar source code?
On Tue, Jan 22, 2013 at 10:52:59AM +, Tony Travis wrote: > >For the tarball itself I have two remarks: > > > > 2. A really large part of the source tarball is a convenience copy of > > the seqan library which is also packages in seqan-dev package. > > Usually we try strongly to build packages against Debian packaged > > libraries and thus I would be very happy if we could drop the > > seqan code (by at the same time tweaking src/CMakeLists.txt to > > regard the Debian packaged seqan.) Unfortunately the included > > copy has some indifferent state - it is way younger than the latest > > official seqan release (1.3.1) which is packaged. So the question > > remains whether flexbar will really build with Debian's seqan > > package. It is the duty of the Debian maintainer of flexbar to > > find this out (either by testing himself or by asking upstream.) > > I've discussed this with Johannes already off-list, and I was able > to compile his source release unmodified on Bio-Linux 7/Ubuntu 12.04 > LTS. OK, lets see how things evolve regarding the seqan library. BTW, I will consider changing the packaging of seqan anyway because it does not fit the usual packaging scheme of libraries (but that's post Wheezy release work.) Kind regards and thanks for your work on flexbar Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130123124555.ge9...@an3as.eu
Re: Flexbar source code?
On 21/01/13 21:17, Andreas Tille wrote: [...] Before I come to the tarball itself: I do not consider it a clever way if you exchange provate mails with upstream author and by doing so proxying mail discussion. Upstream can post in public to the list (his mail address will be uncovered to spammers thought) without subscribing and we can CC him. Hi, Andreas. I was in contact with Johannes Röhr, one of the the upstream authors, before suggesting that we package "Flexbar" for Debian-Med. My initial contact with you about "Flexbar" was off-list and, as you suggested, I moved our conversation about it onto the Debian-Med list. I volunteered to do the packaging because Johannes is too busy. It seems strange to me that you expect an upstream author to take part in online discussions when they are not the package maintainer, but I'll ask Johannes if he will join in the discussion about "Flexbar" here. For the tarball itself I have two remarks: 1. It would be a good idea to include a file COPYING containing the license statement. 2. A really large part of the source tarball is a convenience copy of the seqan library which is also packages in seqan-dev package. Usually we try strongly to build packages against Debian packaged libraries and thus I would be very happy if we could drop the seqan code (by at the same time tweaking src/CMakeLists.txt to regard the Debian packaged seqan.) Unfortunately the included copy has some indifferent state - it is way younger than the latest official seqan release (1.3.1) which is packaged. So the question remains whether flexbar will really build with Debian's seqan package. It is the duty of the Debian maintainer of flexbar to find this out (either by testing himself or by asking upstream.) I've discussed this with Johannes already off-list, and I was able to compile his source release unmodified on Bio-Linux 7/Ubuntu 12.04 LTS. apt-cache policy seqan-dev seqan-dev: Installed: 1.3.1-0ubuntu1 Candidate: 1.3.1-0ubuntu1 Version table: *** 1.3.1-0ubuntu1 0 500 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ precise/main amd64 Packages 100 /var/lib/dpkg/status 1.3-1ubuntu2 0 500 http://gb.archive.ubuntu.com/ubuntu/ precise/universe amd64 Packages If Johannes is willing to join in the discussion, I will let him continue. Otherwise, I'll post a summary of my off-list discussions with him about "Flexbar" dependencies. Bye, Tony. -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/50fe6f8b.1010...@minke.ukfsn.org
Re: Flexbar source code?
Hi Tony, On Mon, Jan 21, 2013 at 03:09:01PM +, Tony Travis wrote: > >rsync -aP flexbar_v2.31_src.tgz ajtravis-gu...@alioth.debian.org:src/Flexbar/ I fetched it from there successfully. > Perhaps it should have gone into: > > ~/incoming > > Please let me know what the Alioth etiquette is for doing uploads. There is no such thing like an etiquette for your Alioth home directory. Providing things there is not the usual way to go (I personally never did) but it worked in this specific case. > I've not used Git myself, other than to check-out other people's > sources. I'm happy to use either git or svn for the "flexbar" > package. So I might decide depending from the outcome of this source tarball decision. If we need to change it in some way perhaps Git might be the better choice. Before I come to the tarball itself: I do not consider it a clever way if you exchange provate mails with upstream author and by doing so proxying mail discussion. Upstream can post in public to the list (his mail address will be uncovered to spammers thought) without subscribing and we can CC him. For the tarball itself I have two remarks: 1. It would be a good idea to include a file COPYING containing the license statement. 2. A really large part of the source tarball is a convenience copy of the seqan library which is also packages in seqan-dev package. Usually we try strongly to build packages against Debian packaged libraries and thus I would be very happy if we could drop the seqan code (by at the same time tweaking src/CMakeLists.txt to regard the Debian packaged seqan.) Unfortunately the included copy has some indifferent state - it is way younger than the latest official seqan release (1.3.1) which is packaged. So the question remains whether flexbar will really build with Debian's seqan package. It is the duty of the Debian maintainer of flexbar to find this out (either by testing himself or by asking upstream.) Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130121211754.ge20...@an3as.eu
Re: Flexbar source code?
On 20/01/13 15:54, Andreas Tille wrote: [...] Johannes will make the source tarball available for download on SourceForge, but wants us to look at it first and is willing to make changes that would make it easier to package. Sound he is quite responsive. Hmmm, well if he wants us to have a look first it might be one option that you put it on alioth and tell us here if done (and the path of the file.) Hi, Andreas. OK, I uploaded the Flexbar source tarball provided by Johannes: rsync -aP flexbar_v2.31_src.tgz ajtravis-gu...@alioth.debian.org:src/Flexbar/ Perhaps it should have gone into: ~/incoming Please let me know what the Alioth etiquette is for doing uploads. BTW, do you prefer SVN or Git for maintaining the package on Alioth? Id had some spare cycles on Friday and started something at svn://svn.debian.org/debian-med/trunk/packages/flexbar/trunk/ but if you prefer Git we should move this to Git once we have a source tarball. I've not used Git myself, other than to check-out other people's sources. I'm happy to use either git or svn for the "flexbar" package. Bye, Tony. -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/50fd5a0d.8070...@minke.ukfsn.org
Re: Flexbar source code?
Hi Tony, On Sun, Jan 20, 2013 at 02:01:48PM +, Tony Travis wrote: > Hi, Andreas and Diane. > > The upstream author Johannes Röhr has created source tarball and > emailed it to me. Should I upload this to my account on Allioth? > > Johannes will make the source tarball available for download on > SourceForge, but wants us to look at it first and is willing to make > changes that would make it easier to package. Sound he is quite responsive. Hmmm, well if he wants us to have a look first it might be one option that you put it on alioth and tell us here if done (and the path of the file.) BTW, do you prefer SVN or Git for maintaining the package on Alioth? Id had some spare cycles on Friday and started something at svn://svn.debian.org/debian-med/trunk/packages/flexbar/trunk/ but if you prefer Git we should move this to Git once we have a source tarball. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130120155440.ga26...@an3as.eu
Re: Flexbar source code?
On 18/01/13 23:20, Andreas Tille wrote: Hi Tony, On Fri, Jan 18, 2013 at 03:52:04PM +, Tony Travis wrote: Can we not just export a snapshot of their SVN version? Diane has given a perfect answer and I can only agree with her: Sure we can - but not all we can is reasonable and I see no reason to ask for trouble just in the beginning. Hi, Andreas and Diane. The upstream author Johannes Röhr has created source tarball and emailed it to me. Should I upload this to my account on Allioth? Johannes will make the source tarball available for download on SourceForge, but wants us to look at it first and is willing to make changes that would make it easier to package. Bye, Tony. -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/50fbf8cc.7080...@minke.ukfsn.org
Re: Flexbar source code? (Was: feature request)
On 18/01/13 18:20, Diane Trout wrote:
debian in general likes there to be official releases. A lot of the
packaging tools are designed around tracking specific versioned
tarballs. to make releases repeatable there needs to at least be tagged
versions. Though tarballs would be better.
Hi, Diane.
OK, I'll ask the developers to provide an official source tarball.
Bye,
Tony.
DianeOn 1/18/13 7:52 Tony Travis wrote:
On 18/01/13 14:43, Andreas Tille wrote:
[...]
Could you please contact the authors / those who asked you for the
packaging to care for a versioned source code tarball besides their
binary download files. (And yes, we could checkout from SVN but
it is better to avoid this to safe us from extra hassle.)
Hi, Andreas.
Can we not just export a snapshot of their SVN version?
For example:
#!/bin/bash
# @(#)SVN 2013-01-18 A.J.Travis
#
# Checkout current SVN version and export a clean source snapshot
#
VERSION=$(svn info svn://svn.code.sf.net/p/flexbar/code | awk '/Revision/{print
$2}')
svn checkout svn://svn.code.sf.net/p/flexbar/code/trunk flexbar-code
svn export svn://svn.code.sf.net/p/flexbar/code/trunk flexbar_src_v2.$VERSION
tar jcf flexbar_src_v2.$VERSION.tgz flexbar_src_v2.$VERSION
This is how I got the sources I'm using on our Bio-Linux server in
Edinburgh.
This would be a precondition for our packaging work and we should
make sure that we will be able to start smoothly without spending
time into things like this.
Well, since it's me who wants to package their software for Debian-Med
and Bio-Linux I think I should make the effort to smooth things along!
See you in Kiel
Indeed, I'm looking forward to the meeting!
Bye,
Tony.
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Re: Flexbar source code? (Was: feature request)
Hi Tony, On Fri, Jan 18, 2013 at 03:52:04PM +, Tony Travis wrote: > Can we not just export a snapshot of their SVN version? Diane has given a perfect answer and I can only agree with her: Sure we can - but not all we can is reasonable and I see no reason to ask for trouble just in the beginning. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130118232049.gb12...@an3as.eu
Re: Flexbar source code? (Was: feature request)
debian in general likes there to be official releases. A lot of the packaging
tools are designed around tracking specific versioned tarballs. to make
releases repeatable there needs to at least be tagged versions. Though tarballs
would be better.
DianeOn 1/18/13 7:52 Tony Travis wrote:
On 18/01/13 14:43, Andreas Tille wrote:
> [...]
> Could you please contact the authors / those who asked you for the
> packaging to care for a versioned source code tarball besides their
> binary download files. (And yes, we could checkout from SVN but
> it is better to avoid this to safe us from extra hassle.)
Hi, Andreas.
Can we not just export a snapshot of their SVN version?
For example:
> #!/bin/bash
> # @(#)SVN 2013-01-18 A.J.Travis
>
> #
> # Checkout current SVN version and export a clean source snapshot
> #
> VERSION=$(svn info svn://svn.code.sf.net/p/flexbar/code | awk
> '/Revision/{print $2}')
>
> svn checkout svn://svn.code.sf.net/p/flexbar/code/trunk flexbar-code
> svn export svn://svn.code.sf.net/p/flexbar/code/trunk flexbar_src_v2.$VERSION
> tar jcf flexbar_src_v2.$VERSION.tgz flexbar_src_v2.$VERSION
This is how I got the sources I'm using on our Bio-Linux server in
Edinburgh.
> This would be a precondition for our packaging work and we should
> make sure that we will be able to start smoothly without spending
> time into things like this.
Well, since it's me who wants to package their software for Debian-Med
and Bio-Linux I think I should make the effort to smooth things along!
> See you in Kiel
Indeed, I'm looking forward to the meeting!
Bye,
Tony.
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Re: Flexbar source code? (Was: feature request)
On 18/01/13 14:43, Andreas Tille wrote:
[...]
Could you please contact the authors / those who asked you for the
packaging to care for a versioned source code tarball besides their
binary download files. (And yes, we could checkout from SVN but
it is better to avoid this to safe us from extra hassle.)
Hi, Andreas.
Can we not just export a snapshot of their SVN version?
For example:
#!/bin/bash
# @(#)SVN 2013-01-18 A.J.Travis
#
# Checkout current SVN version and export a clean source snapshot
#
VERSION=$(svn info svn://svn.code.sf.net/p/flexbar/code | awk '/Revision/{print
$2}')
svn checkout svn://svn.code.sf.net/p/flexbar/code/trunk flexbar-code
svn export svn://svn.code.sf.net/p/flexbar/code/trunk flexbar_src_v2.$VERSION
tar jcf flexbar_src_v2.$VERSION.tgz flexbar_src_v2.$VERSION
This is how I got the sources I'm using on our Bio-Linux server in
Edinburgh.
This would be a precondition for our packaging work and we should
make sure that we will be able to start smoothly without spending
time into things like this.
Well, since it's me who wants to package their software for Debian-Med
and Bio-Linux I think I should make the effort to smooth things along!
See you in Kiel
Indeed, I'm looking forward to the meeting!
Bye,
Tony.
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Archive: http://lists.debian.org/50f96fa4.9090...@minke.ukfsn.org
Flexbar source code? (Was: feature request)
Hi Tony On Wed, Jan 16, 2013 at 02:16:03PM +, Tony Travis wrote: > > ... > > http://debian-med.alioth.debian.org/tasks/bio ? > > > >flexbar is not on the list - so until now nobody considered packaging. I gave flexbar a very quick look and noticed, that there is no source tarball at ist download page https://sourceforge.net/projects/flexbar/files/2.31/ Could you please contact the authors / those who asked you for the packaging to care for a versioned source code tarball besides their binary download files. (And yes, we could checkout from SVN but it is better to avoid this to safe us from extra hassle.) This would be a precondition for our packaging work and we should make sure that we will be able to start smoothly without spending time into things like this. See you in Kiel Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130118144336.ga...@an3as.eu
