From aengus.stewart at cancer.org.uk Wed Sep 1 07:07:52 2010 From: aengus.stewart at cancer.org.uk (Aengus Stewart) Date: Wed, 01 Sep 2010 12:07:52 +0100 Subject: [EMBOSS] dbxflat problem - no more In-Reply-To: <45956.86.26.12.63.1283251940.squirrel@webmail.ebi.ac.uk> References: <6967ac4e0812100700s3708c00br7dbc606e79a6529c@mail.gmail.com> <4C7CC63E.2050007@cancer.org.uk> <45956.86.26.12.63.1283251940.squirrel@webmail.ebi.ac.uk> Message-ID: <4C7E3408.4040105@cancer.org.uk> Hi Alan, Problem has gone away! I had a cronjob that hadnt finished and so there were 2 dbxflat processes trying to write to the same files. Needless to say things got a little confused and I got that error message....... Just need to be a bit more careful. Cheers Aengus -- ----------------------------------------------------------------------- Aengus Stewart Tel: +44 (0)20 7269 3679 Head of Bioinformatics and BioStatistics CRUK London Research Institute Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK ----------------------------------------------------------------------- This electronic message contains information which may be privileged and confidential. The information is intended to be for the use of the individual(s) or entity named above. Be aware that any third party disclosure, distribution, copying or use of this communication, without prior permission, is strictly prohibited. This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. Our central telephone number is 020 7242 0200. >From 1 October 2010 our registered address will be Angel Building, 407 St John Street, London, EC1V 4AD. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. From conrad.h.halling at monsanto.com Fri Sep 3 10:32:47 2010 From: conrad.h.halling at monsanto.com (HALLING, CONRAD H [AG/2076]) Date: Fri, 3 Sep 2010 10:32:47 -0400 Subject: [EMBOSS] Virus/Malware Signal in mEMBOSS-6.3.1.2-setup.exe Message-ID: <8F039817F666C24BB296C135151ED7EE07533DFF@NA2551EXM01.na.ds.monsanto.com> One of my colleagues downloaded the mEMBOSS-6.3.1.2-setup.exe installer for Windows EMBOSS. When she ran the installer, the Trend Micro Office Scan antivirus software that we use quarantined a file, which blocked the installation. The Virus/Malware Name detected was WORM_STRAT.GEN-3, and the file in which the signal was detected was C:\mEMBOSS\is-4GB6P.tmp. This may be a false hit, but can someone check this installer? In the meantime, we are going to install from an older version. Conrad Halling, Ph.D. Senior Bioinformatics Scientist Protein Optimization Platform Protein Technologies Program Monsanto Company 245 First Street, Suite 200 Cambridge, MA 02142 -------------- next part -------------- This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited. All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto, including its subsidiaries. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto, along with its subsidiaries, accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment. The information contained in this email may be subject to the export control laws and regulations of the United States, potentially including but not limited to the Export Administration Regulations ("EAR") and sanctions regulations issued by the U.S. Department of Treasury, Office of Foreign Asset Controls (?OFAC?). As a recipient of this information you are obligated to comply with all applicable U.S. export laws and regulations. From ajb at ebi.ac.uk Fri Sep 3 13:02:35 2010 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Fri, 3 Sep 2010 18:02:35 +0100 (BST) Subject: [EMBOSS] Virus/Malware Signal in mEMBOSS-6.3.1.2-setup.exe In-Reply-To: <8F039817F666C24BB296C135151ED7EE07533DFF@NA2551EXM01.na.ds.monsanto.c om> References: <8F039817F666C24BB296C135151ED7EE07533DFF@NA2551EXM01.na.ds.monsanto.com> Message-ID: <49325.86.26.12.63.1283533355.squirrel@webmail.ebi.ac.uk> Hello Conrad, The mEMBOSS-6.3.1.2-setup.exe is clean according to the latest, updated, AVG-free (9.0.851) both as a file and for a complete computer scan after its installation. Also, though not primarily a virus/work scanner, Windows Defender reports the same machine to be clean. The filename, is-4GB6P.tmp, suggests it is a temporary file produced by the Inno Setup installer, used by mEMBOSS. It is not part of (m)EMBOSS itself and does not appear after installation. The computer used for creating the mEMBOSS exe is not routinely used for accessing the internet. HTH Alan > One of my colleagues downloaded the mEMBOSS-6.3.1.2-setup.exe installer > for Windows EMBOSS. When she ran the installer, the Trend Micro Office > Scan antivirus software that we use quarantined a file, which blocked > the installation. The Virus/Malware Name detected was WORM_STRAT.GEN-3, > and the file in which the signal was detected was > C:\mEMBOSS\is-4GB6P.tmp. > > > > This may be a false hit, but can someone check this installer? > > > > In the meantime, we are going to install from an older version. > > > > Conrad Halling, Ph.D. > > Senior Bioinformatics Scientist > > Protein Optimization Platform > > Protein Technologies Program > > Monsanto Company > > 245 First Street, Suite 200 > > Cambridge, MA 02142 > > > > > This e-mail message may contain privileged and/or confidential > information, and is intended to be received only by persons entitled to > receive such information. If you have received this e-mail in error, > please notify the sender immediately. Please delete it and all attachments > from any servers, hard drives or any other media. Other use of this e-mail > by you is strictly prohibited. > > All e-mails and attachments sent and received are subject to monitoring, > reading and archival by Monsanto, including its subsidiaries. The > recipient of this e-mail is solely responsible for checking for the > presence of "Viruses" or other "Malware". Monsanto, along with its > subsidiaries, accepts no liability for any damage caused by any such code > transmitted by or accompanying this e-mail or any attachment. > > > The information contained in this email may be subject to the export > control laws and regulations of the United States, potentially including > but not limited to the Export Administration Regulations ("EAR") and > sanctions regulations issued by the U.S. Department of Treasury, Office of > Foreign Asset Controls (???OFAC???). As a recipient of this information > you are obligated to comply with all applicable U.S. export laws and > regulations. > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From tothg at abc.hu Mon Sep 6 07:01:31 2010 From: tothg at abc.hu (Gabor Toth) Date: Mon, 6 Sep 2010 13:01:31 +0200 Subject: [EMBOSS] accessing emboss ftp site In-Reply-To: <4C50193D.5060500@bioteam.net> References: <6F57C2D1-8927-420C-940C-C6EC0C62AABE@gmail.com> <4C50193D.5060500@bioteam.net> Message-ID: <201009061301.31442.tothg@abc.hu> wget times out after issuing the 'LIST -a' command. wget 1.11.4 / Linux (openSUSE 11.2 x86_64) Gabor On Wed July 28 2010 13:49:17 Chris Dagdigian wrote: > I can't seem to replicate this at all with any of my available FTP > clients or browser-based FTP clients. It works for me from both Mac OS X > clients as well as a CentOS 5.4 based Linux system. > > Is there an FTP client / OS combo that seems in particular not to work? > > -Chris > > Here is one example: > > dag-static:~ dag$ ftp emboss.open-bio.org > > Connected to emboss.open-bio.org. > > 220 (vsFTPd 2.0.1) > > Name (emboss.open-bio.org:dag): anonymous > > 331 Please specify the password. > > Password: > > 230 Login successful. > > Remote system type is UNIX. > > Using binary mode to transfer files. > > ftp> dir > > 229 Entering Extended Passive Mode (|||54472|) > > 150 Here comes the directory listing. > > drwxr-xr-x 8 14 50 4096 May 22 2006 pub > > 226 Directory send OK. > > ftp> cd pub/EMBOSS > > 250 Directory successfully changed. > > ftp> ls > > 229 Entering Extended Passive Mode (|||38343|) > > 150 Here comes the directory listing. > > -rw-rw-r-- 1 501 503 389856 Jul 21 09:25 > > CBSTOOLS-1.0.0.tar.gz -rw-rw-r-- 1 501 503 426218 Jul 21 > > 09:25 DOMAINATRIX-0.1.0.tar.gz -rw-rw-r-- 1 501 503 441025 > > Jul 21 09:25 DOMALIGN-0.1.0.tar.gz -rw-rw-r-- 1 501 503 > > 452787 Jul 21 09:25 DOMSEARCH-0.1.0.tar.gz -rw-rw-r-- 1 501 503 > > 23572243 Jul 19 13:41 EMBOSS-6.3.1.tar.gz lrwxrwxrwx 1 501 503 > > 19 Jul 19 13:42 EMBOSS-latest.tar.gz -> EMBOSS-6.3.1.tar.gz > > -rw-rw-r-- 1 501 503 373798 Jul 21 09:25 EMNU-1.05.tar.gz > > -rw-rw-r-- 1 501 503 415096 Jul 21 09:25 > > ESIM4-1.0.0.tar.gz -rw-rw-r-- 1 501 503 569581 Jul 21 > > 09:25 HMMER-2.3.2.tar.gz -rw-rw-r-- 1 501 503 350791 Jul > > 21 09:25 IPRSCAN-4.3.1.tar.gz drwxrwsr-x 7 501 503 4096 > > Feb 01 2006 Jemboss > > -rw-rw-r-- 1 501 503 513418 Jul 21 09:25 > > MEMENEW-4.0.0.tar.gz -rw-rw-r-- 1 501 503 823636 Jul 21 > > 09:25 MIRA-2.8.2.tar.gz -rw-rw-r-- 1 501 503 435315 Jul 21 > > 09:25 MSE-3.0.0.tar.gz -rw-rw-r-- 1 501 503 328540 Jul 21 > > 09:25 MYEMBOSS-6.3.0.tar.gz -rw-rw-r-- 1 501 503 359488 > > Jul 21 09:25 MYEMBOSSDEMO-6.3.0.tar.gz -rw-rw-r-- 1 501 503 > > 1667760 Jul 21 09:25 PHYLIPNEW-3.69.tar.gz -rw-rw-r-- 1 501 503 > > 571008 Jul 21 09:25 SIGNATURE-0.1.0.tar.gz -rw-rw-r-- 1 501 > > 503 531604 Jul 21 09:25 STRUCTURE-0.1.0.tar.gz -rw-rw-r-- 1 501 > > 503 386287 Jul 21 09:25 TOPO-2.0.0.tar.gz -rw-rw-r-- 1 501 > > 503 652433 Jul 21 09:25 VIENNA-1.7.2.tar.gz drwxrwsr-x 3 > > 522 503 4096 Aug 21 2006 contrib > > drwxrwsr-x 2 501 503 4096 Nov 11 2005 doc > > drwxrwsr-x 3 501 503 4096 Jul 21 09:25 fixes > > drwxrwsr-x 14 501 503 4096 Jul 19 13:39 old > > drwxrwsr-x 2 501 503 4096 Jul 06 2005 tutorials > > drwxrwsr-x 4 501 503 4096 Jul 19 13:36 windows > > 226 Directory send OK. > > ftp> > > Hamish McWilliam wrote: > > Hi Chris, > > > > I'm also seeing problems with the FTP site, but using Mirror rather > > than Transmit, it looks like the server does not like options being > > specified to the LIST command: > > > > Scanning remote directory /pub/EMBOSS > > ---> CWD /pub/EMBOSS > > 250 Directory successfully changed. > > ---> TYPE A > > 200 Switching to ASCII mode. > > ---> PORT 172,21,22,1,171,245 > > 200 PORT command successful. Consider using PASV. > > ---> PASV > > 227 Entering Passive Mode (208,94,50,58,104,178) > > ---> LIST -lat > > timed out > > Cannot get remote directory listing because: timed out > > Cannot get remote directory details (/pub/EMBOSS) > > disconnecting from emboss.open-bio.org > > > > Trying it with a command line client I get the response to hang if I > > try using any options to ls or dir, without options they are fine. > > > > All the best, > > > > Hamish > > > > On 29 May 2010 03:44, Koen van der Drift wrote: > >> Hi Chris, > >> > >> Did you have a chance to look at this? Just tried again, and Transmit > >> still won't let me access the emboss ftp site. > >> > >> Thanks, > >> > >> - Koen. > >> > >> On Apr 23, 2010, at 11:44 AM, Chris Dagdigian wrote: > >>> In the last few months the open-bio.org servers switched datacenters, > >>> IP addresses and firewall/IDS appliances. Lots of juicy things to look > >>> at and debug. > >>> > >>> Koen - if you have a chance can you send me the IP address that you are > >>> using to connect from? I might be able to find some relevant log > >>> entries with that info. > >>> > >>> -Chris > >>> > >>> Koen van der Drift wrote: > >>>> Just for the record, it used to work with Transmit, this is only from > >>>> the last few months. > >>>> > >>>> - Koen. > >>>> > >>>> On Thu, Apr 22, 2010 at 7:28 PM, Chris Dagdigian > >>>> > >>>> wrote: > >>>>> Might be an issue with the Juniper Netscreen firewall/IDS security > >>>>> appliance > >>>>> that sits upstream of the EMBOSS FTP server. I'll take a look at the > >>>>> security logs and alerts. > >>>>> > >>>>> -Chris > >>>>> > >>>>> Koen van der Drift wrote: > >>>>>> Hi, > >>>>>> > >>>>>> For a while now I am unable to access the emboss ftp site using the > >>>>>> OS X > >>>>>> client Transmit. Loggin in works fine, but it chokes on the LIST > >>>>>> command. I have no problems accessing it from the command line. I > >>>>>> have added the output from Transmit below. I don't know if this is a > >>>>>> Transmit > >>>>>> or emboss issue, but just wanted to let you know. > >>>>>> > >>>>>> Thanks, > >>>>>> > >>>>>> - Koen. > >>>>>> > >>>>>> > >>>>>> Transmit 3.6.9 Session Transcript > >>>>>> LibNcFTP 3.2.1 (August 13, 2007) compiled for UNIX > >>>>>> Uname: Darwin|exile.local|9.8.0|Darwin Kernel Version 9.8.0: Wed Jul > >>>>>> 15 16:57:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_PPC|Power > >>>>>> Macintosh 220: (vsFTPd 2.0.1) > >>>>>> Connected to emboss.open-bio.org. > >>>>>> Cmd: USER anonymous > >>>>>> 331: Please specify the password. > >>>>>> Cmd: PASS NcFTP@ > >>>>>> 230: Login successful. > >>>>>> Cmd: TYPE A > >>>>>> 200: Switching to ASCII mode. > >>>>>> Logged in to emboss.open-bio.org as anonymous. > >>>>>> Cmd: SYST > >>>>>> 215: UNIX Type: L8 > >>>>>> Cmd: PWD > >>>>>> 257: "/" > >>>>>> Cmd: CWD /pub/EMBOSS/fixes > >>>>>> 250: Directory successfully changed. > >>>>>> Cmd: PWD > >>>>>> 257: "/pub/EMBOSS/fixes" > >>>>>> Cmd: PASV > >>>>>> 227: Entering Passive Mode (208,94,50,58,83,232) > >>>>>> Cmd: LIST -a > >>>>>> Could not read reply from control connection -- timed out. > >>>>>> (SReadline 1) > >>>>>> 220: (vsFTPd 2.0.1) > >>>>>> Connected to emboss.open-bio.org. > >>>>>> Cmd: USER anonymous > >>>>>> 331: Please specify the password. > >>>>>> Cmd: PASS NcFTP@ > >>>>>> 230: Login successful. > >>>>>> Logged in to emboss.open-bio.org as anonymous. > >>>>>> Cmd: SYST > >>>>>> 215: UNIX Type: L8 > >>>>>> Cmd: PWD > >>>>>> 257: "/" > >>>>>> Cmd: CWD /pub/EMBOSS/fixes > >>>>>> 250: Directory successfully changed. > >>>>>> Cmd: PWD > >>>>>> 257: "/pub/EMBOSS/fixes" > >>>>>> Cmd: PASV > >>>>>> 227: Entering Passive Mode (208,94,50,58,222,100) > >>>>>> Cmd: LIST -a > >>>>>> Could not read reply from control connection -- timed out. > >>>>>> (SReadline 1) > >>>>>> > >>>>>> _______________________________________________ > >>>>>> EMBOSS mailing list > >>>>>> EMBOSS at lists.open-bio.org > >>>>>> http://lists.open-bio.org/mailman/listinfo/emboss > >> > >> _______________________________________________ > >> EMBOSS mailing list > >> EMBOSS at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/emboss > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From gbottu at vub.ac.be Tue Sep 7 14:13:44 2010 From: gbottu at vub.ac.be (Guy Bottu) Date: Tue, 07 Sep 2010 20:13:44 +0200 Subject: [EMBOSS] wrappers4EMBOSS 2.5.0 released Message-ID: <4C8680D8.6000306@vub.ac.be> Dear users of wrappers4EMBOSS, version 2.5.0 of wrappers4EMBOSS has just been released. It has been adapted to support EMBOSS version 6.3. It was necessary to modify some ACD files since from EMBOSS 6.3.0 on parameters of which the minimum or maximum allowed value depend on other parameters demand a special treatment. Regards, Guy Bottu, wEMBOSS development team From aengus.stewart at cancer.org.uk Wed Sep 1 11:07:52 2010 From: aengus.stewart at cancer.org.uk (Aengus Stewart) Date: Wed, 01 Sep 2010 12:07:52 +0100 Subject: [EMBOSS] dbxflat problem - no more In-Reply-To: <45956.86.26.12.63.1283251940.squirrel@webmail.ebi.ac.uk> References: <6967ac4e0812100700s3708c00br7dbc606e79a6529c@mail.gmail.com> <4C7CC63E.2050007@cancer.org.uk> <45956.86.26.12.63.1283251940.squirrel@webmail.ebi.ac.uk> Message-ID: <4C7E3408.4040105@cancer.org.uk> Hi Alan, Problem has gone away! I had a cronjob that hadnt finished and so there were 2 dbxflat processes trying to write to the same files. Needless to say things got a little confused and I got that error message....... Just need to be a bit more careful. Cheers Aengus -- ----------------------------------------------------------------------- Aengus Stewart Tel: +44 (0)20 7269 3679 Head of Bioinformatics and BioStatistics CRUK London Research Institute Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK ----------------------------------------------------------------------- This electronic message contains information which may be privileged and confidential. The information is intended to be for the use of the individual(s) or entity named above. Be aware that any third party disclosure, distribution, copying or use of this communication, without prior permission, is strictly prohibited. This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. Our central telephone number is 020 7242 0200. >From 1 October 2010 our registered address will be Angel Building, 407 St John Street, London, EC1V 4AD. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. From conrad.h.halling at monsanto.com Fri Sep 3 14:32:47 2010 From: conrad.h.halling at monsanto.com (HALLING, CONRAD H [AG/2076]) Date: Fri, 3 Sep 2010 10:32:47 -0400 Subject: [EMBOSS] Virus/Malware Signal in mEMBOSS-6.3.1.2-setup.exe Message-ID: <8F039817F666C24BB296C135151ED7EE07533DFF@NA2551EXM01.na.ds.monsanto.com> One of my colleagues downloaded the mEMBOSS-6.3.1.2-setup.exe installer for Windows EMBOSS. When she ran the installer, the Trend Micro Office Scan antivirus software that we use quarantined a file, which blocked the installation. The Virus/Malware Name detected was WORM_STRAT.GEN-3, and the file in which the signal was detected was C:\mEMBOSS\is-4GB6P.tmp. This may be a false hit, but can someone check this installer? In the meantime, we are going to install from an older version. Conrad Halling, Ph.D. Senior Bioinformatics Scientist Protein Optimization Platform Protein Technologies Program Monsanto Company 245 First Street, Suite 200 Cambridge, MA 02142 -------------- next part -------------- This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited. All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto, including its subsidiaries. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto, along with its subsidiaries, accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment. The information contained in this email may be subject to the export control laws and regulations of the United States, potentially including but not limited to the Export Administration Regulations ("EAR") and sanctions regulations issued by the U.S. Department of Treasury, Office of Foreign Asset Controls (?OFAC?). As a recipient of this information you are obligated to comply with all applicable U.S. export laws and regulations. From ajb at ebi.ac.uk Fri Sep 3 17:02:35 2010 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Fri, 3 Sep 2010 18:02:35 +0100 (BST) Subject: [EMBOSS] Virus/Malware Signal in mEMBOSS-6.3.1.2-setup.exe In-Reply-To: <8F039817F666C24BB296C135151ED7EE07533DFF@NA2551EXM01.na.ds.monsanto.c om> References: <8F039817F666C24BB296C135151ED7EE07533DFF@NA2551EXM01.na.ds.monsanto.com> Message-ID: <49325.86.26.12.63.1283533355.squirrel@webmail.ebi.ac.uk> Hello Conrad, The mEMBOSS-6.3.1.2-setup.exe is clean according to the latest, updated, AVG-free (9.0.851) both as a file and for a complete computer scan after its installation. Also, though not primarily a virus/work scanner, Windows Defender reports the same machine to be clean. The filename, is-4GB6P.tmp, suggests it is a temporary file produced by the Inno Setup installer, used by mEMBOSS. It is not part of (m)EMBOSS itself and does not appear after installation. The computer used for creating the mEMBOSS exe is not routinely used for accessing the internet. HTH Alan > One of my colleagues downloaded the mEMBOSS-6.3.1.2-setup.exe installer > for Windows EMBOSS. When she ran the installer, the Trend Micro Office > Scan antivirus software that we use quarantined a file, which blocked > the installation. The Virus/Malware Name detected was WORM_STRAT.GEN-3, > and the file in which the signal was detected was > C:\mEMBOSS\is-4GB6P.tmp. > > > > This may be a false hit, but can someone check this installer? > > > > In the meantime, we are going to install from an older version. > > > > Conrad Halling, Ph.D. > > Senior Bioinformatics Scientist > > Protein Optimization Platform > > Protein Technologies Program > > Monsanto Company > > 245 First Street, Suite 200 > > Cambridge, MA 02142 > > > > > This e-mail message may contain privileged and/or confidential > information, and is intended to be received only by persons entitled to > receive such information. If you have received this e-mail in error, > please notify the sender immediately. Please delete it and all attachments > from any servers, hard drives or any other media. Other use of this e-mail > by you is strictly prohibited. > > All e-mails and attachments sent and received are subject to monitoring, > reading and archival by Monsanto, including its subsidiaries. The > recipient of this e-mail is solely responsible for checking for the > presence of "Viruses" or other "Malware". Monsanto, along with its > subsidiaries, accepts no liability for any damage caused by any such code > transmitted by or accompanying this e-mail or any attachment. > > > The information contained in this email may be subject to the export > control laws and regulations of the United States, potentially including > but not limited to the Export Administration Regulations ("EAR") and > sanctions regulations issued by the U.S. Department of Treasury, Office of > Foreign Asset Controls (???OFAC???). As a recipient of this information > you are obligated to comply with all applicable U.S. export laws and > regulations. > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From tothg at abc.hu Mon Sep 6 11:01:31 2010 From: tothg at abc.hu (Gabor Toth) Date: Mon, 6 Sep 2010 13:01:31 +0200 Subject: [EMBOSS] accessing emboss ftp site In-Reply-To: <4C50193D.5060500@bioteam.net> References: <6F57C2D1-8927-420C-940C-C6EC0C62AABE@gmail.com> <4C50193D.5060500@bioteam.net> Message-ID: <201009061301.31442.tothg@abc.hu> wget times out after issuing the 'LIST -a' command. wget 1.11.4 / Linux (openSUSE 11.2 x86_64) Gabor On Wed July 28 2010 13:49:17 Chris Dagdigian wrote: > I can't seem to replicate this at all with any of my available FTP > clients or browser-based FTP clients. It works for me from both Mac OS X > clients as well as a CentOS 5.4 based Linux system. > > Is there an FTP client / OS combo that seems in particular not to work? > > -Chris > > Here is one example: > > dag-static:~ dag$ ftp emboss.open-bio.org > > Connected to emboss.open-bio.org. > > 220 (vsFTPd 2.0.1) > > Name (emboss.open-bio.org:dag): anonymous > > 331 Please specify the password. > > Password: > > 230 Login successful. > > Remote system type is UNIX. > > Using binary mode to transfer files. > > ftp> dir > > 229 Entering Extended Passive Mode (|||54472|) > > 150 Here comes the directory listing. > > drwxr-xr-x 8 14 50 4096 May 22 2006 pub > > 226 Directory send OK. > > ftp> cd pub/EMBOSS > > 250 Directory successfully changed. > > ftp> ls > > 229 Entering Extended Passive Mode (|||38343|) > > 150 Here comes the directory listing. > > -rw-rw-r-- 1 501 503 389856 Jul 21 09:25 > > CBSTOOLS-1.0.0.tar.gz -rw-rw-r-- 1 501 503 426218 Jul 21 > > 09:25 DOMAINATRIX-0.1.0.tar.gz -rw-rw-r-- 1 501 503 441025 > > Jul 21 09:25 DOMALIGN-0.1.0.tar.gz -rw-rw-r-- 1 501 503 > > 452787 Jul 21 09:25 DOMSEARCH-0.1.0.tar.gz -rw-rw-r-- 1 501 503 > > 23572243 Jul 19 13:41 EMBOSS-6.3.1.tar.gz lrwxrwxrwx 1 501 503 > > 19 Jul 19 13:42 EMBOSS-latest.tar.gz -> EMBOSS-6.3.1.tar.gz > > -rw-rw-r-- 1 501 503 373798 Jul 21 09:25 EMNU-1.05.tar.gz > > -rw-rw-r-- 1 501 503 415096 Jul 21 09:25 > > ESIM4-1.0.0.tar.gz -rw-rw-r-- 1 501 503 569581 Jul 21 > > 09:25 HMMER-2.3.2.tar.gz -rw-rw-r-- 1 501 503 350791 Jul > > 21 09:25 IPRSCAN-4.3.1.tar.gz drwxrwsr-x 7 501 503 4096 > > Feb 01 2006 Jemboss > > -rw-rw-r-- 1 501 503 513418 Jul 21 09:25 > > MEMENEW-4.0.0.tar.gz -rw-rw-r-- 1 501 503 823636 Jul 21 > > 09:25 MIRA-2.8.2.tar.gz -rw-rw-r-- 1 501 503 435315 Jul 21 > > 09:25 MSE-3.0.0.tar.gz -rw-rw-r-- 1 501 503 328540 Jul 21 > > 09:25 MYEMBOSS-6.3.0.tar.gz -rw-rw-r-- 1 501 503 359488 > > Jul 21 09:25 MYEMBOSSDEMO-6.3.0.tar.gz -rw-rw-r-- 1 501 503 > > 1667760 Jul 21 09:25 PHYLIPNEW-3.69.tar.gz -rw-rw-r-- 1 501 503 > > 571008 Jul 21 09:25 SIGNATURE-0.1.0.tar.gz -rw-rw-r-- 1 501 > > 503 531604 Jul 21 09:25 STRUCTURE-0.1.0.tar.gz -rw-rw-r-- 1 501 > > 503 386287 Jul 21 09:25 TOPO-2.0.0.tar.gz -rw-rw-r-- 1 501 > > 503 652433 Jul 21 09:25 VIENNA-1.7.2.tar.gz drwxrwsr-x 3 > > 522 503 4096 Aug 21 2006 contrib > > drwxrwsr-x 2 501 503 4096 Nov 11 2005 doc > > drwxrwsr-x 3 501 503 4096 Jul 21 09:25 fixes > > drwxrwsr-x 14 501 503 4096 Jul 19 13:39 old > > drwxrwsr-x 2 501 503 4096 Jul 06 2005 tutorials > > drwxrwsr-x 4 501 503 4096 Jul 19 13:36 windows > > 226 Directory send OK. > > ftp> > > Hamish McWilliam wrote: > > Hi Chris, > > > > I'm also seeing problems with the FTP site, but using Mirror rather > > than Transmit, it looks like the server does not like options being > > specified to the LIST command: > > > > Scanning remote directory /pub/EMBOSS > > ---> CWD /pub/EMBOSS > > 250 Directory successfully changed. > > ---> TYPE A > > 200 Switching to ASCII mode. > > ---> PORT 172,21,22,1,171,245 > > 200 PORT command successful. Consider using PASV. > > ---> PASV > > 227 Entering Passive Mode (208,94,50,58,104,178) > > ---> LIST -lat > > timed out > > Cannot get remote directory listing because: timed out > > Cannot get remote directory details (/pub/EMBOSS) > > disconnecting from emboss.open-bio.org > > > > Trying it with a command line client I get the response to hang if I > > try using any options to ls or dir, without options they are fine. > > > > All the best, > > > > Hamish > > > > On 29 May 2010 03:44, Koen van der Drift wrote: > >> Hi Chris, > >> > >> Did you have a chance to look at this? Just tried again, and Transmit > >> still won't let me access the emboss ftp site. > >> > >> Thanks, > >> > >> - Koen. > >> > >> On Apr 23, 2010, at 11:44 AM, Chris Dagdigian wrote: > >>> In the last few months the open-bio.org servers switched datacenters, > >>> IP addresses and firewall/IDS appliances. Lots of juicy things to look > >>> at and debug. > >>> > >>> Koen - if you have a chance can you send me the IP address that you are > >>> using to connect from? I might be able to find some relevant log > >>> entries with that info. > >>> > >>> -Chris > >>> > >>> Koen van der Drift wrote: > >>>> Just for the record, it used to work with Transmit, this is only from > >>>> the last few months. > >>>> > >>>> - Koen. > >>>> > >>>> On Thu, Apr 22, 2010 at 7:28 PM, Chris Dagdigian > >>>> > >>>> wrote: > >>>>> Might be an issue with the Juniper Netscreen firewall/IDS security > >>>>> appliance > >>>>> that sits upstream of the EMBOSS FTP server. I'll take a look at the > >>>>> security logs and alerts. > >>>>> > >>>>> -Chris > >>>>> > >>>>> Koen van der Drift wrote: > >>>>>> Hi, > >>>>>> > >>>>>> For a while now I am unable to access the emboss ftp site using the > >>>>>> OS X > >>>>>> client Transmit. Loggin in works fine, but it chokes on the LIST > >>>>>> command. I have no problems accessing it from the command line. I > >>>>>> have added the output from Transmit below. I don't know if this is a > >>>>>> Transmit > >>>>>> or emboss issue, but just wanted to let you know. > >>>>>> > >>>>>> Thanks, > >>>>>> > >>>>>> - Koen. > >>>>>> > >>>>>> > >>>>>> Transmit 3.6.9 Session Transcript > >>>>>> LibNcFTP 3.2.1 (August 13, 2007) compiled for UNIX > >>>>>> Uname: Darwin|exile.local|9.8.0|Darwin Kernel Version 9.8.0: Wed Jul > >>>>>> 15 16:57:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_PPC|Power > >>>>>> Macintosh 220: (vsFTPd 2.0.1) > >>>>>> Connected to emboss.open-bio.org. > >>>>>> Cmd: USER anonymous > >>>>>> 331: Please specify the password. > >>>>>> Cmd: PASS NcFTP@ > >>>>>> 230: Login successful. > >>>>>> Cmd: TYPE A > >>>>>> 200: Switching to ASCII mode. > >>>>>> Logged in to emboss.open-bio.org as anonymous. > >>>>>> Cmd: SYST > >>>>>> 215: UNIX Type: L8 > >>>>>> Cmd: PWD > >>>>>> 257: "/" > >>>>>> Cmd: CWD /pub/EMBOSS/fixes > >>>>>> 250: Directory successfully changed. > >>>>>> Cmd: PWD > >>>>>> 257: "/pub/EMBOSS/fixes" > >>>>>> Cmd: PASV > >>>>>> 227: Entering Passive Mode (208,94,50,58,83,232) > >>>>>> Cmd: LIST -a > >>>>>> Could not read reply from control connection -- timed out. > >>>>>> (SReadline 1) > >>>>>> 220: (vsFTPd 2.0.1) > >>>>>> Connected to emboss.open-bio.org. > >>>>>> Cmd: USER anonymous > >>>>>> 331: Please specify the password. > >>>>>> Cmd: PASS NcFTP@ > >>>>>> 230: Login successful. > >>>>>> Logged in to emboss.open-bio.org as anonymous. > >>>>>> Cmd: SYST > >>>>>> 215: UNIX Type: L8 > >>>>>> Cmd: PWD > >>>>>> 257: "/" > >>>>>> Cmd: CWD /pub/EMBOSS/fixes > >>>>>> 250: Directory successfully changed. > >>>>>> Cmd: PWD > >>>>>> 257: "/pub/EMBOSS/fixes" > >>>>>> Cmd: PASV > >>>>>> 227: Entering Passive Mode (208,94,50,58,222,100) > >>>>>> Cmd: LIST -a > >>>>>> Could not read reply from control connection -- timed out. > >>>>>> (SReadline 1) > >>>>>> > >>>>>> _______________________________________________ > >>>>>> EMBOSS mailing list > >>>>>> EMBOSS at lists.open-bio.org > >>>>>> http://lists.open-bio.org/mailman/listinfo/emboss > >> > >> _______________________________________________ > >> EMBOSS mailing list > >> EMBOSS at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/emboss > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From gbottu at vub.ac.be Tue Sep 7 18:13:44 2010 From: gbottu at vub.ac.be (Guy Bottu) Date: Tue, 07 Sep 2010 20:13:44 +0200 Subject: [EMBOSS] wrappers4EMBOSS 2.5.0 released Message-ID: <4C8680D8.6000306@vub.ac.be> Dear users of wrappers4EMBOSS, version 2.5.0 of wrappers4EMBOSS has just been released. It has been adapted to support EMBOSS version 6.3. It was necessary to modify some ACD files since from EMBOSS 6.3.0 on parameters of which the minimum or maximum allowed value depend on other parameters demand a special treatment. Regards, Guy Bottu, wEMBOSS development team