Re: [spctools-discuss] raw conversion to mzml on win 7- 64 bit

2011-03-03 Thread Joe Slagel
quot; group. > To post to this group, send email to spctools-discuss@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. >

Re: [spctools-discuss] -Etrypsin error and ReAdW error.

2011-02-28 Thread Joe Slagel
ps > "spctools-discuss" group. > To post to this group, send email to spctools-discuss@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/spctoo

Re: [spctools-discuss] trapper ion type problem

2011-02-25 Thread Joe Slagel
pctools-discuss" group. > To post to this group, send email to spctools-discuss@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/spctoo

Re: [spctools-discuss] non-vendor centroiding?

2011-02-10 Thread Joe Slagel
To post to this group, send email to spctools-discuss@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- Joe S

Re: [spctools-discuss] Problem in Installation TPP

2011-01-28 Thread Joe Slagel
hat process named "httpd" on the list. My Windows is vista > version. > Do I need to install the Apache? > > Thanks, > > Yoona > > On Fri, Jan 28, 2011 at 10:08 AM, Joe Slagel > wrote: > >> On Windows, you should see an little Apache services icon in yo

Re: [spctools-discuss] Problem in Installation TPP

2011-01-28 Thread Joe Slagel
, visit this group at >> > http://groups.google.com/group/spctools-discuss?hl=en. >> > >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To post to this group, send email to sp

Re: [spctools-discuss] Problem in Installation TPP

2011-01-28 Thread Joe Slagel
o the Google Groups > > "spctools-discuss" group. > > To post to this group, send email to spctools-discuss@googlegroups.com. > > To unsubscribe from this group, send email to > > spctools-discuss+unsubscr...@googlegroups.com > . > > For more options, visit th

Re: [spctools-discuss] All tools fail in gui but most of them work on the command line.

2011-01-24 Thread Joe Slagel
message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to spctools-discuss@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com > . > For

Re: [spctools-discuss] add/create account for GUI under Ubuntu

2011-01-24 Thread Joe Slagel
Groups > "spctools-discuss" group. > To post to this group, send email to spctools-discuss@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com > . > For more options, visit this group at > http://groups.

Re: [spctools-discuss] Operation not permitted

2011-01-05 Thread Joe Slagel
ibed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to spctools-disc...@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com > . > For more options, visit this group at > http://gro

Re: [spctools-discuss] pepXML and protXML format

2010-12-10 Thread Joe Slagel
Department of Structural Biology and Bioinformatics > University Medical Center (CMU), University of Geneva > 1 rue Michel Servet, 1211 Geneva 4, Switzerland > Phone: +41 (0)22 379 41 69 > Fax: +41 (0)22 379 55 02 > Email: christine.hoogl...@unige.ch > --

Re: [spctools-discuss] how to run iprophet with many input files?

2010-12-08 Thread Joe Slagel
BTW, in the example where I use "ls *", you may actually need to do a "find . -name '*.pep.xml' -maxdepth 2". On Wed, Dec 8, 2010 at 2:54 PM, Joe Slagel wrote: > Andreas, > > There are a couple of options that I can think of depending on exactly what > y

Re: [spctools-discuss] how to run iprophet with many input files?

2010-12-08 Thread Joe Slagel
:-)! > > cheers, > andreas > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to spctools-disc...@googlegroups.com. > To unsubscribe from this group, send email to &g

Re: [spctools-discuss] mzwiff converter question

2010-11-22 Thread Joe Slagel
spctools-discuss+unsubscr...@googlegroups.com > . > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- Joe Slagel Institute for Systems Biology jsla...@systemsbiology.org (206) 732-1362 -- You received this message because you are subscr

Re: [spctools-discuss] Re: FOR command to process conversion of .raw to .mzXML in batch with massWolf

2010-11-12 Thread Joe Slagel
age (http://tools.proteomecenter.org/ > wiki/index.php?title=Msconvert_Capabilities<http://tools.proteomecenter.org/%0Awiki/index.php?title=Msconvert_Capabilities>). > It does work with > MassLynx .raw files, right? > > Thanks, > Sam > > On Nov 12, 2:14 pm, Joe Slagel wrote: >

Re: [spctools-discuss] FOR command to process conversion of .raw to .mzXML in batch with massWolf

2010-11-12 Thread Joe Slagel
post to this group, send email to spctools-disc...@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com > . > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- Joe Slagel

Re: [spctools-discuss] file permissions under Petunia/Windows

2010-11-05 Thread Joe Slagel
Groups > "spctools-discuss" group. > To post to this group, send email to spctools-disc...@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com > . > For more options, visit this group at > http://groups.google.c

Re: [spctools-discuss] can't open any file

2010-11-01 Thread Joe Slagel
discuss" group. > To post to this group, send email to spctools-disc...@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com > . > For more options, visit this group at > http://groups.google.com/group/sp

[spctools-discuss] Announcing TPP release: 4.4.1

2010-10-29 Thread Joe Slagel
eadme file in TPP/src as well as the wiki. The TPP Team: Luis, David, Joe, Eric, Brian, Natalie, and Jimmy plus all other developers who contributed to this release from the ISB. Thanks to developers and users from the TPP's user community who provided feedback and code cont

Re: [spctools-discuss] Reference for input arguments

2010-09-03 Thread Joe Slagel
s > "spctools-discuss" group. > To post to this group, send email to spctools-disc...@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com > . > For more options, visit this group at > http://groups.google.com/grou

Re: [spctools-discuss] Q3ProteinRatioParser

2010-08-27 Thread Joe Slagel
. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com > . > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- Joe Slagel Institute for Systems Biology jsla...@systemsbiology.org (206)

Re: [spctools-discuss] install problem for tpp 4.4.0 on centos

2010-08-25 Thread Joe Slagel
/singleton.hpp: >>> At global scope: >>> /cluster/apps/tpp/4.4.0/src/../extern/ProteoWizard/pwiz/libraries/boost_aux/boost/utility/singleton.hpp:176: >>> error: wrong number of template arguments (2, should be 3) >>> /cluster/apps/tpp/4.4.0/src/../extern/Proteo

Re: [spctools-discuss] Re: MSConvert Error

2010-08-24 Thread Joe Slagel
To post to this group, send email to spctools-disc...@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com > . > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > --

Re: [spctools-discuss] TPP 4.4.0 build on Linux

2010-08-17 Thread Joe Slagel
40/src/../build/linux/PepcView/ > PepcView.html] Error 1 > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to spctools-disc...@googlegroups.com. > To unsubscribe from thi

Re: [spctools-discuss] RefreshParser error with Myrimatch

2010-08-12 Thread Joe Slagel
10_08.fasta"" >> >>> >> >>> command "C:/Inetpub/tpp-bin/RefreshParser "myri_test_interact.pep.xml" >> >>> "C:\Inetpub\wwwroot\ISB\data\dbase >> >>> \uniprot_human_CP_canonical_isoform_cRAP_decoy_2010_08.fasta"&qu

Re: [spctools-discuss] Is TPP incompatible with Perl 5.12 ?

2010-07-09 Thread Joe Slagel
>>> >>> -- >>> You received this message because you are subscribed to the Google Groups >>> "spctools-discuss" group. >>> To post to this group, send email to spctools-disc...@googlegroups.com. >>> To unsubscribe from this group, send email to

Re: [spctools-discuss] Is TPP incompatible with Perl 5.12 ?

2010-07-09 Thread Joe Slagel
ore options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- Joe Slagel Institute for Systems Biology jsla...@systemsbiology.org (206) 732-1362 -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. T

Re: [spctools-discuss] Distribution of ReAdW.exe

2010-06-24 Thread Joe Slagel
ols-discuss+unsubscr...@googlegroups.com > . > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- Joe Slagel Institute for Systems Biology jsla...@systemsbiology.org (206) 732-1362 -- You received this message because you are sub

Re: [spctools-discuss] Re: Unresolved issue: TPP GUI error message: sh: tpp_hostname: command not found

2010-06-01 Thread Joe Slagel
; this? > > > > >> >> > > >> > -- > > >> >> > > >> > You received this message because you are subscribed to > the > > >> >> > > >> > Google > > >> >> > > Groups >

Re: [spctools-discuss] Re: Unresolved issue: TPP GUI error message: sh: tpp_hostname: command not found

2010-05-24 Thread Joe Slagel
;;, and in your check_env.pl output the HTTP_HOST is listed as "host". Are you perhaps using virtual hosts in your Apache configuration? - -- Joe Slagel Institute for Systems Biology jsla...@systemsbiology.org (206) 732-1362 -- You received this message because you are subscribed to

Re: [spctools-discuss] Converting .RAW files

2010-03-09 Thread Joe Slagel
pctools-discuss" group. > To post to this group, send email to spctools-disc...@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com > . > For more options, visit this group at > http://groups.google.com/group/spc

Re: [spctools-discuss] Msconvert vs Trapper - Speed differences and preprocessing

2010-02-17 Thread Joe Slagel
e preprocessing that isn't >> strictly necessary, for Agilent ".d" files at least? >> >> Thanks, >> bio.x2y >> >> >> > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discu

Re: [spctools-discuss] Official location of mzXML schema files

2010-02-16 Thread Joe Slagel
d email to > spctools-discuss+unsubscr...@googlegroups.com > . > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- Joe Slagel Institute for Systems Biology jsla...@systemsbiology.org (206) 732-1362 -- You received this messag

Re: [spctools-discuss] Re: problems with converting files to mzXML with trapper

2010-01-26 Thread Joe Slagel
B.01.04). > > > > > Sincerely > > > > > Mauri > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to spctools-disc...@googlegroups.com. > To unsubsc

Re: [spctools-discuss] New install of TPP - can't access /tpp/html ?

2009-11-23 Thread Joe Slagel
d! > > - Austin > > -- > > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to spctools-disc...@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+

[spctools-discuss] Re: problem converting with trapper 4.3.1 on windows vista 64bit

2009-10-07 Thread Joe Slagel
red inside files > of course as MSPeak.bin or MSProfile.bin. IIRC you can pass it any of > those three (the .d directory, or the .bin files). Also, a MassHunter > installation is not required for either trapper or msconvert - it makes > no difference. > > -Matt > > > Joe Slagel

[spctools-discuss] Re: problem converting with trapper 4.3.1 on windows vista 64bit

2009-10-06 Thread Joe Slagel
ce trapper in the near future. > > -Natalie > > > > > On Oct 6, 2009, at 3:29 PM, Joe Slagel wrote: > > Hi all, > > One of our users also just ran into the exact same problem. Her system has > .Net framework 3.5sp1, TPP 4.3.1, trapper, and the MassHunter (B1.03?) &

[spctools-discuss] Re: problem converting with trapper 4.3.1 on windows vista 64bit

2009-10-06 Thread Joe Slagel
ed3.d > c:\andreasquandt\data\E_QTOF\E09_100209_RS_fasted3.c.mzXML > > ERROR at .\MHDACWrapper.cpp, 49: > HR = -2147221164 > ERROR - CoCreateInstance failed. > unable to open c:\andreasquandt\data\E_QTOF\E09_100209_RS_fasted3.d with > MassHun > ter interface > > would be great if anyone co

[spctools-discuss] Re: Failure with make

2009-09-28 Thread Joe Slagel
Debian Etch server. > > Eliza. > > On Sep 26, 1:20 am, Joe Slagel wrote: > > Eliza, > > > > I may have another alternative for you, but I can't make any promises > it'll > > work. I played around a little today with building rpb/deb packages for > &

[spctools-discuss] Re: Failure with make

2009-09-25 Thread Joe Slagel
ackage that will work for you. To install it, use dpkg as so: % dpkg -i tpp_4.3.1-1_amd64.deb The default installation location is /usr/tpp. Cheers, Joe P.S. You should consider it very *EXPERIMENTAL* as I only tested a few simple operations. On Fri, Sep 25, 2009 at 2:00 PM, Joe Slagel wrot

[spctools-discuss] Re: Failure with make

2009-09-25 Thread Joe Slagel
> > > >>>>>> [mailto:spctools-disc...@googlegroups.com] On Behalf Of Eliza > > > > >>>>>> Sent: Thursday, August 27, 2009 12:13 AM > > > > >>>>>> To: spctools-discuss > > > &g

[spctools-discuss] Re: Question about TPP 4.3.0 apache2 configuration on ubuntu 9.04

2009-09-02 Thread Joe Slagel
er allow,deny >Allow from all > > Alias /tandem/ "/var/www/thegpm/tandem/" > > >Options Indexes MultiViews >AllowOverride None > Order allow,deny >Allow from all > > Alias /cache/ "/var

[spctools-discuss] Re: Question about TPP 4.3.0 apache2 configuration on ubuntu 9.04

2009-09-01 Thread Joe Slagel
oceeding with undefined results > [Sat Aug 29 17:41:45 2009] [warn] NameVirtualHost *:80 has no > VirtualHosts > > [ OK ] > - > Does this point me towards where I am going wrong? > Regards, > Achim > > On Aug 25, 10:39 pm, J

[spctools-discuss] Re: Question about TPP 4.3.0 apache2 configuration on ubuntu 9.04

2009-08-25 Thread Joe Slagel
-- > The requested URL /tpp/cgi-bin/tpp_gui.pl was not found on this > server. > Apache/2.2.11 (Ubuntu) PHP/5.2.6-3ubuntu4.2 with Suhosin-Patch Server > at linux01 Port 80 > ------ > > Thanks a million

[spctools-discuss] Re: Question about TPP 4.3.0 apache2 configuration on ubuntu 9.04

2009-08-25 Thread Joe Slagel
ml > drwxr-xr-x 2 root root 4096 2009-08-24 11:13 tppschema > end terminal output ------- > > Does this indicate that I have done something wrong during the > installation process or that the file structure might have changed > slightly, without t

[spctools-discuss] Re: installation problems on ubuntu 9.04

2009-08-21 Thread Joe Slagel
terminal ------- > > Anybody's help is very much appreciated. > > Thanks a lot in advance, > > Achim > > -- > Achim Treumann > NEPAF, Newcastle upon Tyne, UK > > > > -- Joe Slagel Institute for Systems Biology jsla...@systemsbiology.org (206) 732-1362

[spctools-discuss] Re: 4.2 build error tpplib_perl.so

2009-08-03 Thread Joe Slagel
PLIB_SWIG -o /root/tpp-4.2.1/src/../build/ > > linux/ > > tpplib_perl_wrap.o ./tpplib/tpplib_perl_wrap.cxx 2> /dev/null > > make[1]: *** [/root/tpp-4.2.1/src/../build/linux/tpplib_perl.so] Error > > 1 > > make[1]: Leaving directory `/root/tpp-4.2.1/src' > > mak

[spctools-discuss] Re: Apache timeout preventing long Sequest searches - fixed

2009-07-22 Thread Joe Slagel
Timeout 18000 > > I changed the timeout to 36 (100 hours) and now I can have > searches running all weekend without stalling. Thanks, Jimmy! > > Do any of the developers know if setting "Timeout 0" or just deleting > that line will eliminate the