From raoul.bonnal at itb.cnr.it Mon Oct 4 09:22:37 2004 From: raoul.bonnal at itb.cnr.it (Raoul Jean Pierre Bonnal) Date: Mon, 04 Oct 2004 15:22:37 +0200 Subject: Different path for acd file Message-ID: <1096894361.4870.29.camel@localhost> hi, I have compiled and installed cvs emboss siute. I've packged my application for debian, so my acd file is under /usr/share/myapp/acd/myapp.acd acd emboss file are installed in /usr/share/EMBOSS/acd when I run my application, the program looks for myapp.acd under /usr/share/EMBOSS/acd and then exit with Error: File /usr/share/EMBOSS/acd/myapp.acd line 0: ACD file not opened I have tried to use into the main of myapp embInitP("myapp", argc, argv, "/usr/share/myapp"); without success. I thought embInitP function would have dynamically modified the standard settings (ref. AJAX_FIXED_ROOT). Is there a solution? If I copy myapp.acd in /usr/share/EMBOSS/acd myapp runs correctly. -- Raoul Jean Pierre Bonnal I.T.B. - C.N.R. via Fratelli Cervi, 93 20090 Segrate -Mi-, Italy Floor 7, Room 13 Tel. +390226422724 Fax. +390226422770 E-mail: raoul.bonnal at itb.cnr.it From pmr at ebi.ac.uk Thu Oct 7 06:49:56 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 07 Oct 2004 11:49:56 +0100 Subject: Different path for acd file In-Reply-To: <1096894361.4870.29.camel@localhost> References: <1096894361.4870.29.camel@localhost> Message-ID: <41651F54.4010204@ebi.ac.uk> Raoul Jean Pierre Bonnal wrote: > hi, > I have compiled and installed cvs emboss siute. > I've packged my application for debian, so my acd file is under > /usr/share/myapp/acd/myapp.acd This is indeed a problem. EMBOSS will look in one directory for ACD files - normally the share/EMBOSS/acd directory under the install directory. You can define another location using environment variables ... but that would be for *all* EMBOSS applications. EMBASSY applications (mse, topo, phylip, end so on) are built under embassy/mse but installed in the same directories as EMBOSS. > acd emboss file are installed in > /usr/share/EMBOSS/acd > > when I run my application, the program looks for myapp.acd under > /usr/share/EMBOSS/acd and then exit with Error: File > /usr/share/EMBOSS/acd/myapp.acd line 0: ACD file not opened > > I have tried to use into the main of myapp > > embInitP("myapp", argc, argv, "/usr/share/myapp"); > > without success. I thought embInitP function would have dynamically > modified the standard settings (ref. AJAX_FIXED_ROOT). embInitP will not modify the standard settings ... and I don't really like a fixed path in the code :-) You can use (csh and tcsh): setenv EMBOSS_ACDROOT /usr/share/myapp/acd/ ... but that redefines the location for all ACD files. > Is there a solution? > > If I copy myapp.acd in /usr/share/EMBOSS/acd myapp runs correctly. That is the solution we would recommend. We could find ways to code around it and offer an alternative directory to search ... but it would slow down all other applications, and you can expect problems with finding data files if too many directories have to be searched. From henrikki.almusa at helsinki.fi Mon Oct 11 03:39:00 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Mon, 11 Oct 2004 10:39:00 +0300 Subject: Pattern lists In-Reply-To: <200408100939.24959.henrikki.almusa@helsinki.fi> References: <200408100939.24959.henrikki.almusa@helsinki.fi> Message-ID: <200410111039.00010.henrikki.almusa@helsinki.fi> Hello, I would be happy if I could get the pattern list things moving onwards. So reposting my questions from a while back. I could use the pattern lists already, with fuzznuc after some changes. I haven't attached the patches (ajpat.c, ajpath, nucleus/embpat.patch and emboss/fuzznuc.patch) in this post, but can post them again if wanted. On Tuesday 10 August 2004 09:39, Henrikki Almusa wrote: > 1. How to do the acd overloading. In my patch to dreg and fuzznuc, I used > string and then did what was needed in program. This is not probably the > correct way, but ok for testing. > > 2. Should I add a search function into pattern lists? This would allow > fuzz(nuc|pro|tran) to run regular expression pattern as well (thus > obsoleting dreg and preg). This change would also mean that patterns in > files would need a attribute as well (value might a number > or string). But this might cause confusion as mismatch values don't work > with regexes (even though it would be there). > > 3. Is it ok to use '#include ../nucleus/emboss.h' in 'ajpat.c'? This was > done as I needed functions from 'nucleus/embpat.h'. If this is not how it > should be done then how? > > 4. Any thing else that needs to be fixed for inclusion into emboss? Any > namings or such? Make the functions more similar to AjPFeattable (eg. > ajPatternNew would put it to pattern list as well? > Any help on these would be appreciated, -- Henrikki Almusa From raoul.bonnal at itb.cnr.it Mon Oct 4 13:22:37 2004 From: raoul.bonnal at itb.cnr.it (Raoul Jean Pierre Bonnal) Date: Mon, 04 Oct 2004 15:22:37 +0200 Subject: Different path for acd file Message-ID: <1096894361.4870.29.camel@localhost> hi, I have compiled and installed cvs emboss siute. I've packged my application for debian, so my acd file is under /usr/share/myapp/acd/myapp.acd acd emboss file are installed in /usr/share/EMBOSS/acd when I run my application, the program looks for myapp.acd under /usr/share/EMBOSS/acd and then exit with Error: File /usr/share/EMBOSS/acd/myapp.acd line 0: ACD file not opened I have tried to use into the main of myapp embInitP("myapp", argc, argv, "/usr/share/myapp"); without success. I thought embInitP function would have dynamically modified the standard settings (ref. AJAX_FIXED_ROOT). Is there a solution? If I copy myapp.acd in /usr/share/EMBOSS/acd myapp runs correctly. -- Raoul Jean Pierre Bonnal I.T.B. - C.N.R. via Fratelli Cervi, 93 20090 Segrate -Mi-, Italy Floor 7, Room 13 Tel. +390226422724 Fax. +390226422770 E-mail: raoul.bonnal at itb.cnr.it From pmr at ebi.ac.uk Thu Oct 7 10:49:56 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 07 Oct 2004 11:49:56 +0100 Subject: Different path for acd file In-Reply-To: <1096894361.4870.29.camel@localhost> References: <1096894361.4870.29.camel@localhost> Message-ID: <41651F54.4010204@ebi.ac.uk> Raoul Jean Pierre Bonnal wrote: > hi, > I have compiled and installed cvs emboss siute. > I've packged my application for debian, so my acd file is under > /usr/share/myapp/acd/myapp.acd This is indeed a problem. EMBOSS will look in one directory for ACD files - normally the share/EMBOSS/acd directory under the install directory. You can define another location using environment variables ... but that would be for *all* EMBOSS applications. EMBASSY applications (mse, topo, phylip, end so on) are built under embassy/mse but installed in the same directories as EMBOSS. > acd emboss file are installed in > /usr/share/EMBOSS/acd > > when I run my application, the program looks for myapp.acd under > /usr/share/EMBOSS/acd and then exit with Error: File > /usr/share/EMBOSS/acd/myapp.acd line 0: ACD file not opened > > I have tried to use into the main of myapp > > embInitP("myapp", argc, argv, "/usr/share/myapp"); > > without success. I thought embInitP function would have dynamically > modified the standard settings (ref. AJAX_FIXED_ROOT). embInitP will not modify the standard settings ... and I don't really like a fixed path in the code :-) You can use (csh and tcsh): setenv EMBOSS_ACDROOT /usr/share/myapp/acd/ ... but that redefines the location for all ACD files. > Is there a solution? > > If I copy myapp.acd in /usr/share/EMBOSS/acd myapp runs correctly. That is the solution we would recommend. We could find ways to code around it and offer an alternative directory to search ... but it would slow down all other applications, and you can expect problems with finding data files if too many directories have to be searched. From henrikki.almusa at helsinki.fi Mon Oct 11 07:39:00 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Mon, 11 Oct 2004 10:39:00 +0300 Subject: Pattern lists In-Reply-To: <200408100939.24959.henrikki.almusa@helsinki.fi> References: <200408100939.24959.henrikki.almusa@helsinki.fi> Message-ID: <200410111039.00010.henrikki.almusa@helsinki.fi> Hello, I would be happy if I could get the pattern list things moving onwards. So reposting my questions from a while back. I could use the pattern lists already, with fuzznuc after some changes. I haven't attached the patches (ajpat.c, ajpath, nucleus/embpat.patch and emboss/fuzznuc.patch) in this post, but can post them again if wanted. On Tuesday 10 August 2004 09:39, Henrikki Almusa wrote: > 1. How to do the acd overloading. In my patch to dreg and fuzznuc, I used > string and then did what was needed in program. This is not probably the > correct way, but ok for testing. > > 2. Should I add a search function into pattern lists? This would allow > fuzz(nuc|pro|tran) to run regular expression pattern as well (thus > obsoleting dreg and preg). This change would also mean that patterns in > files would need a attribute as well (value might a number > or string). But this might cause confusion as mismatch values don't work > with regexes (even though it would be there). > > 3. Is it ok to use '#include ../nucleus/emboss.h' in 'ajpat.c'? This was > done as I needed functions from 'nucleus/embpat.h'. If this is not how it > should be done then how? > > 4. Any thing else that needs to be fixed for inclusion into emboss? Any > namings or such? Make the functions more similar to AjPFeattable (eg. > ajPatternNew would put it to pattern list as well? > Any help on these would be appreciated, -- Henrikki Almusa