Re: Please choose a free license for eigensoft
Hi Alkes, On Thu, Aug 11, 2016 at 11:01:56AM -0400, Alkes Price wrote: > Thank you for flagging these issues. We have now released EIGENSOFT > 6.1.3 with ploteig restored. We have elected to restore the use of > .perl file names for PERL scripts for backwards compatibility. Due to our watch system I realised the new version some days before your mail and the new version is just available in Debian. Thanks for the notification anyway Andreas. -- http://fam-tille.de
Re: Please choose a free license for eigensoft
Dear Andreas, Thank you for flagging these issues. We have now released EIGENSOFT 6.1.3 with ploteig restored. We have elected to restore the use of .perl file names for PERL scripts for backwards compatibility. Sincerely, Alkes On 7/19/16, Andreas Tille wrote: > Hi, > > On Mon, Jul 18, 2016 at 03:06:56PM -0400, Alkes Price wrote: >> Dear Andreas, >> >> We have now released EIGENSOFT 6.1.2 with a new license, per your >> request. > > Thanks a lot for this. While taking care for the packaging I noticed > that the ploteig executable which smartpca.pl is refering to is missing > from this release. > > When checking the code smartpca.pl is also refering to evec2pca-ped.perl > as well as evec2pca.perl - but both scripts are not named .perl but > rather .pl. > > I have a general remark to those .pl extensions. According to the > Debian upstream guide[1] it is not a good idea to add language > extensions to scripts at all (just read the link[1] to learn several > good reasons why). Since I try to follow the Debian standards inside > the packaging I'm moving the real executables that are called by *.pl > wrappers to /usr/lib/eigensoft and keep only the wrappers inside the > user PATH (/usr/bin) while stripping the extensions. The wrappers are > patched to find the files in /usr/lib/eigensoft. To keep the > functionality of possibly existing user scripts in addition the names > with *.pl extension are provided inside /usr/lib/debian-med/bin and a > README is added that will inform users to set their PATH accordingly. > However, I'd recommend to find a similar solution without those > extensions for all eigensoft users for the reasons I pointed to above. > > Another hint: gc.pl (or just gc) is a very generic name that should > not be used. In the Debian package I install it as > > /usr/bin/gc-eigensoft and > /usr/lib/debian-med/bin/gc.pl > > Please consider a better name since the name gc is just choosen by > graphviz. > > Kind regards and thanks again for your cooperation > >Andreas. > > [1] https://wiki.debian.org/UpstreamGuide#Language_extensions_in_scripts > > -- > http://fam-tille.de > -- Dr. Alkes Price, Associate Professor / Associate Member Harvard T.H. Chan School of Public Health, Depts of Epidemiology and Biostatistics Broad Institute of MIT and Harvard, Program in Medical and Population Genetics Building 2, Room 211, 665 Huntington Ave, Boston, MA 02115 apr...@hsph.harvard.edu, phone: 617-432-2262, fax: 617-432-1722 http://www.hsph.harvard.edu/faculty/alkes-price/
Re: Please choose a free license for eigensoft
Hi, On Mon, Jul 18, 2016 at 03:06:56PM -0400, Alkes Price wrote: > Dear Andreas, > > We have now released EIGENSOFT 6.1.2 with a new license, per your request. Thanks a lot for this. While taking care for the packaging I noticed that the ploteig executable which smartpca.pl is refering to is missing from this release. When checking the code smartpca.pl is also refering to evec2pca-ped.perl as well as evec2pca.perl - but both scripts are not named .perl but rather .pl. I have a general remark to those .pl extensions. According to the Debian upstream guide[1] it is not a good idea to add language extensions to scripts at all (just read the link[1] to learn several good reasons why). Since I try to follow the Debian standards inside the packaging I'm moving the real executables that are called by *.pl wrappers to /usr/lib/eigensoft and keep only the wrappers inside the user PATH (/usr/bin) while stripping the extensions. The wrappers are patched to find the files in /usr/lib/eigensoft. To keep the functionality of possibly existing user scripts in addition the names with *.pl extension are provided inside /usr/lib/debian-med/bin and a README is added that will inform users to set their PATH accordingly. However, I'd recommend to find a similar solution without those extensions for all eigensoft users for the reasons I pointed to above. Another hint: gc.pl (or just gc) is a very generic name that should not be used. In the Debian package I install it as /usr/bin/gc-eigensoft and /usr/lib/debian-med/bin/gc.pl Please consider a better name since the name gc is just choosen by graphviz. Kind regards and thanks again for your cooperation Andreas. [1] https://wiki.debian.org/UpstreamGuide#Language_extensions_in_scripts -- http://fam-tille.de
Re: Please choose a free license for eigensoft
Dear Alkes, On Mon, Jul 18, 2016 at 03:06:56PM -0400, Alkes Price wrote: > Dear Andreas, > > We have now released EIGENSOFT 6.1.2 with a new license, per your request. Thanks a lot, that's very helpful. Kind regards Andreas. > Sincerely, > Alkes > > On 6/30/16, Andreas Tille wrote: > > Hello again, > > > > I have not received any response from your side. I wonder whether the > > mail addresses I used are active and if you are involved in the process > > of deciding about a license. > > > > Kind regards > > > > Andreas. > > > > On Mon, May 30, 2016 at 02:10:21PM +0200, Andreas Tille wrote: > >> Hi, > >> > >> I'm writing you on behalf of the Debian Med team which is a group inside > >> Debian with the objective to package free software with relevance in > >> biology and medicine for official Debian. As you might possibly know we > >> have created packages also from eigensoft as you can see on our so > >> called tasks biology page[1]. > >> > >> Since I realised that there is a new version available I wanted to > >> discuss the licensing issue with you before we are upgrading the > >> package. The problem is that the current licensing permits a > >> distribution inside official Debiani. According to the Debian Free > >> Software Guidelines[2] which are widely accepted as Open Source > >> definition the current license is not free since it is restricted to > >> a specific (== non-commercial) use. > >> > >> I wonder whether you might consider changing the licensing to some free > >> license like GPL, BSD or MPL - just anything that has no such > >> restricttion to non-commercial use. You might like to know that several > >> other authors of biologic software recently switched to free licenses > >> (may be most prominently phylib). The advantage for you inside Debian > >> would be a higher visibility of eigensoft (since we distribute it with > >> metapackages) and a way better quality assurance since Debian is running > >> several tools to automatically detect problems inside the distributed > >> software. > >> > >> Another (unrelated) question is whether there are any publications > >> connected to eigensoft. As you can see in the entries of other packages > >> on our tasks page[1] we usually add publications to the scientific > >> software we are packaging. Just let me know if you want me to add such > >> a record for eigensoft. > >> > >> Kind regards and thanks for your cooperation > >> > >> Andreas. > >> > >> [1] http://blends.debian.org/med/tasks/bio#eigensoft > >> [2] https://www.debian.org/social_contract#guidelines > >> > >> -- > >> http://fam-tille.de > >> > >> > > > > -- > > http://fam-tille.de > > > > > -- > Dr. Alkes Price, Associate Professor / Associate Member > Harvard T.H. Chan School of Public Health, Depts of Epidemiology and > Biostatistics > Broad Institute of MIT and Harvard, Program in Medical and Population Genetics > Building 2, Room 211, 665 Huntington Ave, Boston, MA 02115 > apr...@hsph.harvard.edu, phone: 617-432-2262, fax: 617-432-1722 > http://www.hsph.harvard.edu/faculty/alkes-price/ > > -- http://fam-tille.de
Re: Please choose a free license for eigensoft
Dear Andreas, We have now released EIGENSOFT 6.1.2 with a new license, per your request. Sincerely, Alkes On 6/30/16, Andreas Tille wrote: > Hello again, > > I have not received any response from your side. I wonder whether the > mail addresses I used are active and if you are involved in the process > of deciding about a license. > > Kind regards > > Andreas. > > On Mon, May 30, 2016 at 02:10:21PM +0200, Andreas Tille wrote: >> Hi, >> >> I'm writing you on behalf of the Debian Med team which is a group inside >> Debian with the objective to package free software with relevance in >> biology and medicine for official Debian. As you might possibly know we >> have created packages also from eigensoft as you can see on our so >> called tasks biology page[1]. >> >> Since I realised that there is a new version available I wanted to >> discuss the licensing issue with you before we are upgrading the >> package. The problem is that the current licensing permits a >> distribution inside official Debiani. According to the Debian Free >> Software Guidelines[2] which are widely accepted as Open Source >> definition the current license is not free since it is restricted to >> a specific (== non-commercial) use. >> >> I wonder whether you might consider changing the licensing to some free >> license like GPL, BSD or MPL - just anything that has no such >> restricttion to non-commercial use. You might like to know that several >> other authors of biologic software recently switched to free licenses >> (may be most prominently phylib). The advantage for you inside Debian >> would be a higher visibility of eigensoft (since we distribute it with >> metapackages) and a way better quality assurance since Debian is running >> several tools to automatically detect problems inside the distributed >> software. >> >> Another (unrelated) question is whether there are any publications >> connected to eigensoft. As you can see in the entries of other packages >> on our tasks page[1] we usually add publications to the scientific >> software we are packaging. Just let me know if you want me to add such >> a record for eigensoft. >> >> Kind regards and thanks for your cooperation >> >> Andreas. >> >> [1] http://blends.debian.org/med/tasks/bio#eigensoft >> [2] https://www.debian.org/social_contract#guidelines >> >> -- >> http://fam-tille.de >> >> > > -- > http://fam-tille.de > -- Dr. Alkes Price, Associate Professor / Associate Member Harvard T.H. Chan School of Public Health, Depts of Epidemiology and Biostatistics Broad Institute of MIT and Harvard, Program in Medical and Population Genetics Building 2, Room 211, 665 Huntington Ave, Boston, MA 02115 apr...@hsph.harvard.edu, phone: 617-432-2262, fax: 617-432-1722 http://www.hsph.harvard.edu/faculty/alkes-price/
Re: Please choose a free license for eigensoft
Hello again, I have not received any response from your side. I wonder whether the mail addresses I used are active and if you are involved in the process of deciding about a license. Kind regards Andreas. On Mon, May 30, 2016 at 02:10:21PM +0200, Andreas Tille wrote: > Hi, > > I'm writing you on behalf of the Debian Med team which is a group inside > Debian with the objective to package free software with relevance in > biology and medicine for official Debian. As you might possibly know we > have created packages also from eigensoft as you can see on our so > called tasks biology page[1]. > > Since I realised that there is a new version available I wanted to > discuss the licensing issue with you before we are upgrading the > package. The problem is that the current licensing permits a > distribution inside official Debiani. According to the Debian Free > Software Guidelines[2] which are widely accepted as Open Source > definition the current license is not free since it is restricted to > a specific (== non-commercial) use. > > I wonder whether you might consider changing the licensing to some free > license like GPL, BSD or MPL - just anything that has no such > restricttion to non-commercial use. You might like to know that several > other authors of biologic software recently switched to free licenses > (may be most prominently phylib). The advantage for you inside Debian > would be a higher visibility of eigensoft (since we distribute it with > metapackages) and a way better quality assurance since Debian is running > several tools to automatically detect problems inside the distributed > software. > > Another (unrelated) question is whether there are any publications > connected to eigensoft. As you can see in the entries of other packages > on our tasks page[1] we usually add publications to the scientific > software we are packaging. Just let me know if you want me to add such > a record for eigensoft. > > Kind regards and thanks for your cooperation > > Andreas. > > [1] http://blends.debian.org/med/tasks/bio#eigensoft > [2] https://www.debian.org/social_contract#guidelines > > -- > http://fam-tille.de > > -- http://fam-tille.de
Please choose a free license for eigensoft
Hi, I'm writing you on behalf of the Debian Med team which is a group inside Debian with the objective to package free software with relevance in biology and medicine for official Debian. As you might possibly know we have created packages also from eigensoft as you can see on our so called tasks biology page[1]. Since I realised that there is a new version available I wanted to discuss the licensing issue with you before we are upgrading the package. The problem is that the current licensing permits a distribution inside official Debiani. According to the Debian Free Software Guidelines[2] which are widely accepted as Open Source definition the current license is not free since it is restricted to a specific (== non-commercial) use. I wonder whether you might consider changing the licensing to some free license like GPL, BSD or MPL - just anything that has no such restricttion to non-commercial use. You might like to know that several other authors of biologic software recently switched to free licenses (may be most prominently phylib). The advantage for you inside Debian would be a higher visibility of eigensoft (since we distribute it with metapackages) and a way better quality assurance since Debian is running several tools to automatically detect problems inside the distributed software. Another (unrelated) question is whether there are any publications connected to eigensoft. As you can see in the entries of other packages on our tasks page[1] we usually add publications to the scientific software we are packaging. Just let me know if you want me to add such a record for eigensoft. Kind regards and thanks for your cooperation Andreas. [1] http://blends.debian.org/med/tasks/bio#eigensoft [2] https://www.debian.org/social_contract#guidelines -- http://fam-tille.de
