Re: [galaxy-dev] Active Directory Authentication question
Hi Nicola,
Again I appreciate your help Nicola. I dropped the database and created new
one and then I restarted galaxy. Once galaxy is up then I went to the login
page and used the username without the @example.com part as you suggested. Now
I got a different error as shown below. Something to do with the ldap_ad.py
file. Is there anything I need to add to this file? Or this is because of my
configuration file?
galaxy.auth.providers.ldap_ad ERROR 2017-11-13 14:55:50,929 LDAP authenticate:
search exception
Traceback (most recent call last):
File "/gpfs/home/gal_admin/galaxy/lib/galaxy/auth/providers/ldap_ad.py", line
126, in authenticate
l = ldap.initialize(_get_subs(options, 'server', params))
File
"/gpfs/home/gal_admin/galaxy/.venv/lib/python2.7/site-packages/ldap/functions.py",
line 94, in initialize
return LDAPObject(uri,trace_level,trace_file,trace_stack_limit)
File
"/gpfs/home/gal_admin/galaxy/.venv/lib/python2.7/site-packages/ldap/ldapobject.py",
line 79, in __init__
self._l =
ldap.functions._ldap_function_call(ldap._ldap_module_lock,_ldap.initialize,uri)
File
"/gpfs/home/gal_admin/galaxy/.venv/lib/python2.7/site-packages/ldap/functions.py",
line 66, in _ldap_function_call
result = func(*args,**kwargs)
LDAPError: (2, 'No such file or directory')
galaxy.auth DEBUG 2017-11-13 14:55:50,931 Email: , Username , stopping due to
failed non-continue
Hakeem Almabrazi
Senior Software Architect
Sidra Medical and Research Center
Out-Patient Clinic
PO Box 26999 , Al Luqta Street
Education City North Campus
Qatar Foundation
Tel:+974-4003-7458 (ext:37458) | Mobile: +974-7479-4201
halmabr...@sidra.org<mailto:halmabr...@sidra.org> |
www.sidra.org<http://www.sidra.org/>
[Description: C:\Users\fgenevieve\AppData\Local\Microsoft\Windows\Temporary
Internet Files\Content.Outlook\O53SYTUP\Sidra-Logo-Member of QF Short.PNG]
From: Nicola Soranzo [mailto:nicola.sora...@gmail.com] On Behalf Of Nicola
Soranzo
Sent: Monday, November 13, 2017 1:17 PM
To: Hakeem Almabrazi; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Active Directory Authentication question
Hi Hakeem,
since you are using:
True
you need to use your username without the "@mydomain.com" for the first login.
After the first successful login, Galaxy will store the email associated to
your username on the AD server in its user database and you will be able to use
it as an alternative to your username to login.
Cheers,
Nicola
On 12/11/17 10:46, Hakeem Almabrazi wrote:
HI Nicola,
Thank you for your response. I have added your suggestions but still I am
getting the same error; the username is None if I used the
usern...@domian.com<mailto:usern...@domian.com> as a login in the login page.
Here is the error log I keep getting.
galaxy.webapps.galaxy.controllers.user DEBUG 2017-11-12 13:35:38,507
trans.app.config.auth_config_file: ./config/auth_conf.xml
galaxy.auth.providers.ldap_ad DEBUG 2017-11-12 13:35:38,507 LDAP authenticate:
email is useracco...@mydomain.com<mailto:useracco...@mydomain.com>
galaxy.auth.providers.ldap_ad DEBUG 2017-11-12 13:35:38,507 LDAP authenticate:
username is None
galaxy.auth.providers.ldap_ad DEBUG 2017-11-12 13:35:38,507 LDAP authenticate:
options are {'bind-user':
'{sAMAccountName}@research.sidra.local<mailto:sAMAccountName%7d@research.sidra.local>',
'search-fields': 'sAMAccountName,mail', 'login-use-username': 'True',
'allow-register': 'False', 'auto-register-email': '{mail}', 'server': '
myAD.mydomain.example.local ', 'auto-register': 'True', 'search-base':
'cn=Users,dc=mydomian,dc=example,dc=local', 'auto-register-username':
'{sAMAccountName}', 'search-password': 'PASSWORD', 'search-user':
'serviceacct@mydomain.example.local<mailto:serviceacct@mydomain.example.local>',
'bind-password': '{password}', 'allow-password-change': 'False'}
galaxy.auth.providers.ldap_ad DEBUG 2017-11-12 13:35:38,508 LDAP authenticate:
username must be used to login, cannot be None
And here is my updated auth_config.xml file
ldap
False
True
False
myAD.mydomain.example.local
True
sAMAccountName,mail
cn=Users,dc=mydomain,dc=example,dc=local
serviceacct@mydomain.example.local<mailto:serviceacct@mydomain.example.local>
PASSWORD
{sAMAccountName}@mydomain.example.local<mailto:sAMAccountName%7d@mydomain.example.local>
{password}
{sAMAccountName}
{mail}
localdb
true
I will appreciate it if you think the file looks okay to you.
Thank you
Hakeem Almabrazi
Senior Software Architect
Sidra Medical and Research Center
Out-Patient Clinic
PO Box 26999 , Al Luqta Street
Education City North Campus
Qatar Foundation
Tel:+974-4003-7458 (ext:37458) | Mobile: +974-7479-4201
halmabr...@sidra.org<mai
Re: [galaxy-dev] Active Directory Authentication question
HI Nicola,
Thank you for your response. I have added your suggestions but still I am
getting the same error; the username is None if I used the
usern...@domian.com<mailto:usern...@domian.com> as a login in the login page.
Here is the error log I keep getting.
galaxy.webapps.galaxy.controllers.user DEBUG 2017-11-12 13:35:38,507
trans.app.config.auth_config_file: ./config/auth_conf.xml
galaxy.auth.providers.ldap_ad DEBUG 2017-11-12 13:35:38,507 LDAP authenticate:
email is useracco...@mydomain.com
galaxy.auth.providers.ldap_ad DEBUG 2017-11-12 13:35:38,507 LDAP authenticate:
username is None
galaxy.auth.providers.ldap_ad DEBUG 2017-11-12 13:35:38,507 LDAP authenticate:
options are {'bind-user': '{sAMAccountName}@research.sidra.local',
'search-fields': 'sAMAccountName,mail', 'login-use-username': 'True',
'allow-register': 'False', 'auto-register-email': '{mail}', 'server': '
myAD.mydomain.example.local ', 'auto-register': 'True', 'search-base':
'cn=Users,dc=mydomian,dc=example,dc=local', 'auto-register-username':
'{sAMAccountName}', 'search-password': 'PASSWORD', 'search-user':
'serviceacct@mydomain.example.local', 'bind-password': '{password}',
'allow-password-change': 'False'}
galaxy.auth.providers.ldap_ad DEBUG 2017-11-12 13:35:38,508 LDAP authenticate:
username must be used to login, cannot be None
And here is my updated auth_config.xml file
ldap
False
True
False
myAD.mydomain.example.local
True
sAMAccountName,mail
cn=Users,dc=mydomain,dc=example,dc=local
serviceacct@mydomain.example.local
PASSWORD
{sAMAccountName}@mydomain.example.local
{password}
{sAMAccountName}
{mail}
localdb
true
I will appreciate it if you think the file looks okay to you.
Thank you
Hakeem Almabrazi
Senior Software Architect
Sidra Medical and Research Center
Out-Patient Clinic
PO Box 26999 , Al Luqta Street
Education City North Campus
Qatar Foundation
Tel:+974-4003-7458 (ext:37458) | Mobile: +974-7479-4201
halmabr...@sidra.org<mailto:halmabr...@sidra.org> |
www.sidra.org<http://www.sidra.org/>
[Description: C:\Users\fgenevieve\AppData\Local\Microsoft\Windows\Temporary
Internet Files\Content.Outlook\O53SYTUP\Sidra-Logo-Member of QF Short.PNG]
From: Nicola Soranzo [mailto:nicola.sora...@gmail.com] On Behalf Of Nicola
Soranzo
Sent: Thursday, November 09, 2017 5:44 PM
To: Hakeem Almabrazi; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Active Directory Authentication question
Hi Hakeem,
a couple of suggestions:
- allow-register should be False
- I don't see a line with something like
ldap://dc1.example.com , but I suppose you have omitted it
- if your AD server doesn't allow anonymous searches (like in my case), you
need to specify also:
cn=jsmith,ou=People,dc=domain,dc=com
mysecret
- you definitely need to specify an adapted version of these:
{sAMAccountName}@dc1.example.com<mailto:samaccountname...@dc1.example.com>
{password}
{sAMAccountName}
{mail}
Hope that helps!
Cheers,
Nicola
On 09/11/17 11:24, Hakeem Almabrazi wrote:
Hello,
I have installed the latest galaxy and I would like to use the MS Active
Directory 2012 for authentication. I tried to follow the instructions outlined
here https://galaxyproject.org/admin/config/external-user-auth/ without
touching the lib/galaxy/auth/providers/ldap_ad_py since I thought this is
related to ldap not AD.
Here is the exact auth_config.xml file
+
ldap
True
True
False
True
sAMAccountName,mail
dc=dc1,dc=example,dc=com
((objectClass=user)(sAMAccountName={username}))
+
When I try to login using a real user email and pwd, it says "No user of valid
password" in the Galaxy page. And here is the error log I keep getting.
galaxy.webapps.galaxy.controllers.user DEBUG 2017-11-09 13:55:37,940
trans.app.config.auth_config_file: ./config/auth_conf.xml
galaxy.auth.providers.ldap_ad DEBUG 2017-11-09 13:55:37,940 LDAP authenticate:
email is u...@example.com<mailto:u...@example.com>
galaxy.auth.providers.ldap_ad DEBUG 2017-11-09 13:55:37,940 LDAP authenticate:
username is None
galaxy.auth.providers.ldap_ad DEBUG 2017-11-09 13:55:37,940 LDAP authenticate:
options are {'search-fields': 'sAMAccountName,mail', 'login-use-username':
'True', 'allow-register': 'True', 'auto-register': 'True', 'search-base':
'dc=dc1,dc=example,dc=com', 'search-filter':
'(&(objectClass=user)(sAMAccountName={username}))', 'allow-password-change':
'False'}
galaxy.auth.providers.ldap_ad DEBUG 2017-11-09 13:55:37,940 LDAP authenticate:
username must be used to login, cannot be None
galaxy.auth DEBUG 2017-11-09 13:55:37,941 Email: , Use
[galaxy-dev] Active Directory Authentication question
Hello,
I have installed the latest galaxy and I would like to use the MS Active
Directory 2012 for authentication. I tried to follow the instructions outlined
here https://galaxyproject.org/admin/config/external-user-auth/ without
touching the lib/galaxy/auth/providers/ldap_ad_py since I thought this is
related to ldap not AD.
Here is the exact auth_config.xml file
+
ldap
True
True
False
True
sAMAccountName,mail
dc=dc1,dc=example,dc=com
((objectClass=user)(sAMAccountName={username}))
+
When I try to login using a real user email and pwd, it says "No user of valid
password" in the Galaxy page. And here is the error log I keep getting.
galaxy.webapps.galaxy.controllers.user DEBUG 2017-11-09 13:55:37,940
trans.app.config.auth_config_file: ./config/auth_conf.xml
galaxy.auth.providers.ldap_ad DEBUG 2017-11-09 13:55:37,940 LDAP authenticate:
email is u...@example.com
galaxy.auth.providers.ldap_ad DEBUG 2017-11-09 13:55:37,940 LDAP authenticate:
username is None
galaxy.auth.providers.ldap_ad DEBUG 2017-11-09 13:55:37,940 LDAP authenticate:
options are {'search-fields': 'sAMAccountName,mail', 'login-use-username':
'True', 'allow-register': 'True', 'auto-register': 'True', 'search-base':
'dc=dc1,dc=example,dc=com', 'search-filter':
'(&(objectClass=user)(sAMAccountName={username}))', 'allow-password-change':
'False'}
galaxy.auth.providers.ldap_ad DEBUG 2017-11-09 13:55:37,940 LDAP authenticate:
username must be used to login, cannot be None
galaxy.auth DEBUG 2017-11-09 13:55:37,941 Email: , Username , stopping due to
failed non-continue
Is there anything missing from my auth_config.xml file?
I appreciate any kind of help figuring this out.
Best regards,
Hak
Disclaimer: This email and its attachments may be confidential and are intended
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Re: [galaxy-dev] FastQC galaxy issue
Hi, I think it can. I tried it from command line and it worked. -Original Message- From: Björn Grüning [mailto:bjoern.gruen...@gmail.com] Sent: Saturday, September 12, 2015 11:19 AM To: Hakeem Almabrazi; Bjoern Gruening; galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] FastQC galaxy issue Hi, I'm not sure FASTQC can deal with gz files natively. In the documentation I found they use zcat: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/INSTALL.txt So maybe this is your problem? Bjoern > Hi Bjoern, > > Thank you for your response. To answer your question, yes I am running the > fastqc on a compressed file (fastq.gz) but not tarfile. The files are in > the file system and I Link them to galaxy but not “Copying” them, and I > think that is the issue of my problem which I am I am trying to debug. > > Here is what I sent earlier in regard to that, please let me know if you have > any suggestions on how to go about resolving this issue. > > .. > Hi again, > > After struggling with this issue for few days and exhausted all my options, > the only thing that was left was to use the “Copy the file into galaxy” > instead of “Link files into Galaxy” in the loading page. It took while to > copy but after it was done, I noticed the file was decompressed and it size > was (240 GB) instead of the 30GB. > > I re-ran the FastQC tool and it worked. I am not sure if this is a bug in > the copying/linking part or at the FastQC wrapper. > > Has anyone encountered this issue? Can anyone try to link a fastq file and > run the FastQC to confirm what I am seeing? > > It is very important to us that we link the fastq files instead of copying > them into galaxy. > > I appreciate any feedback. > > Regards, > > > > From: Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] > Sent: Friday, September 11, 2015 4:32 PM > To: Hakeem Almabrazi; galaxy-dev@lists.galaxyproject.org > Subject: Re: [galaxy-dev] FastQC galaxy issue > > Hi, > > are you running fastqc on the compressed tarfile? Or is this file unpacked > already when you are running fastqc on it? > > Thanks, > Bjoern > On 10.09.2015 09:39, Hakeem Almabrazi wrote: > Hi, > > I have encountered the following issue when I try to use FastQC tool in > Galaxy. The fastqc file is validated using the fastqvalidator tool and the > same files have been processed by other tools (i.e bwa) without any > complaints about the fastqc . Also, if I ran the fastqc from the command > line it gets executed without any issue too. > > I have updated my galaxy repository in case there is new updates and the > FastQC version is v0.11.2 > > Is this something to do with the FastQC wrapper in galaxy? > > If it helps, the fastq files are in the file system and I link to them into > galaxy using the options Link and Fastqqsanger as data type. > > Any help will be highly appreciated. > ……….. > Fatal error: Exit code 1 () > Failed to process L-20417_S7_L007_R2_001.fastq > uk.ac.babraham.FastQC.Sequence.SequenceFormatException: ID line didn't start > with '@' > at > uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:158) > at uk.ac.babraham.FastQC.Sequence.FastQFile.(FastQFile.java:89) > at > uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:104) > at > uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:62) > at > uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:122) > at > uk.ac.babraham.FastQC.Analysis.OfflineRunner.(OfflineRunner.java:95) > at > uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:308) > Traceback (most recent call last): > File > "/gpfs/home/galaxyadmin/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/8c650f7f76e9/fastqc/rgFastQC.py", > line 162, in > fastqc_runner.run_fastqc() > File > "/gpfs/home/galaxyadmin/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/8c650f7f76e9/fastqc/rgFastQC.py", > line 136, in run_fastqc > self.copy_output_file_to_dataset() > File > "/gpfs/home/galaxyadmin/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/8c650f7f76e9/fastqc/rgFastQC.py", > line 109, in copy_output_file_to_dataset > with open(result_file[0], 'rb') as fsrc: > IndexError: list index out of range > > Disclaimer: This email and its attachments may be confidential and are > intended solely for the use of the individual to whom it is addressed. If you > are not the intended recipient, any reading, printing, storage, disclosure, > copying or any other action taken in respect of
Re: [galaxy-dev] FastQC galaxy issue
Hi again, After struggling with this issue for few days and exhausted all my options, the only thing that was left was to use the "Copy the file into galaxy" instead of "Link files into Galaxy" in the loading page. It took while to copy but after it was done, I noticed the file was decompressed and it size was (240 GB) instead of the 30GB. I re-ran the FastQC tool and it worked. I am not sure if this is a bug in the copying/linking part or at the FastQC wrapper. Has anyone encountered this issue? Can anyone try to link a fastq file and run the FastQC to confirm what I am seeing? It is very important to us that we link the fastq files instead of copying them into galaxy. I appreciate any feedback. Regards, Hakeem From: galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] On Behalf Of Hakeem Almabrazi Sent: Thursday, September 10, 2015 10:40 AM To: galaxy-dev@lists.galaxyproject.org Subject: [galaxy-dev] FastQC galaxy issue Hi, I have encountered the following issue when I try to use FastQC tool in Galaxy. The fastqc file is validated using the fastqvalidator tool and the same files have been processed by other tools (i.e bwa) without any complaints about the fastqc . Also, if I ran the fastqc from the command line it gets executed without any issue too. I have updated my galaxy repository in case there is new updates and the FastQC version is v0.11.2 Is this something to do with the FastQC wrapper in galaxy? If it helps, the fastq files are in the file system and I link to them into galaxy using the options Link and Fastqqsanger as data type. Any help will be highly appreciated. ... Fatal error: Exit code 1 () Failed to process L-20417_S7_L007_R2_001.fastq uk.ac.babraham.FastQC.Sequence.SequenceFormatException: ID line didn't start with '@' at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:158) at uk.ac.babraham.FastQC.Sequence.FastQFile.(FastQFile.java:89) at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:104) at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:62) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:122) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.(OfflineRunner.java:95) at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:308) Traceback (most recent call last): File "/gpfs/home/galaxyadmin/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/8c650f7f76e9/fastqc/rgFastQC.py", line 162, in fastqc_runner.run_fastqc() File "/gpfs/home/galaxyadmin/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/8c650f7f76e9/fastqc/rgFastQC.py", line 136, in run_fastqc self.copy_output_file_to_dataset() File "/gpfs/home/galaxyadmin/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/8c650f7f76e9/fastqc/rgFastQC.py", line 109, in copy_output_file_to_dataset with open(result_file[0], 'rb') as fsrc: IndexError: list index out of range Disclaimer: This email and its attachments may be confidential and are intended solely for the use of the individual to whom it is addressed. If you are not the intended recipient, any reading, printing, storage, disclosure, copying or any other action taken in respect of this e-mail is prohibited and may be unlawful. If you are not the intended recipient, please notify the sender immediately by using the reply function and then permanently delete what you have received. Any views or opinions expressed are solely those of the author and do not necessarily represent those of Sidra Medical and Research Center. Disclaimer: This email and its attachments may be confidential and are intended solely for the use of the individual to whom it is addressed. If you are not the intended recipient, any reading, printing, storage, disclosure, copying or any other action taken in respect of this e-mail is prohibited and may be unlawful. If you are not the intended recipient, please notify the sender immediately by using the reply function and then permanently delete what you have received. Any views or opinions expressed are solely those of the author and do not necessarily represent those of Sidra Medical and Research Center. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] loading with Auto detect and fastqsanger options issue!
Thank you Martin for your reply. I will give it a try. Can you please send me the name of the tool you are referring to? Also, I am hoping others will be able to share their insights about the other concerns in my post. Regards, From: Martin Vickers [mjv08] [mailto:mj...@aber.ac.uk] Sent: Saturday, September 05, 2015 12:31 PM To: Hakeem Almabrazi Cc: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] loading with Auto detect and fastqsanger options issue! Hi Hak, I noticed the same thing when linking them when adding fastq.gz files as a data library. The auto detect was reading the whole file as it was unknown, presumably looking for some sort of characteristic to place it. What I did to resolve this was add the archive data format data type from the tool shed which included fastq.gz. This meant that auto detect instantly found the correct type. Finally I added the gunzip tool to galaxy and it works well. There is also a trello feature request asking for this to be inbuilt of if you're interested you may wish to vote for it. I will forward you the like when I'm back at a computer. Hope that helps, Martin Sent on the move. On 4 Sep 2015, at 19:04, Hakeem Almabrazi <halmabr...@sidra.org<mailto:halmabr...@sidra.org>> wrote: Hi, I have installed Galaxy as cluster in my local env. I have few fastq.gz files in my file system that I want to link them to galaxy instead of loading them. When I select "Auto Detect" during the loading I noticed two things. First, it is taking way longer to link the files with the AutoDetect option compared to when I chose Fastqsanger as my file type. It takes less than a second if I specify the type, i.e Fastqsanger. Any reason why is that? Is there a way to speed up the first option (Auto Detect)? Second, when it finish linking for AutoDetect option, it shows the DataType for these files as "data" rather than fastq files. Does this mean my fastq.gz files are not recognize as fastq files? To validate my fastq files, I tried to use FastqValidator tool I get an error saying "BGZF EOF marker is missing". How can I fix these files? I appreciate any kind of help, Regards, Hak Disclaimer: This email and its attachments may be confidential and are intended solely for the use of the individual to whom it is addressed. If you are not the intended recipient, any reading, printing, storage, disclosure, copying or any other action taken in respect of this e-mail is prohibited and may be unlawful. If you are not the intended recipient, please notify the sender immediately by using the reply function and then permanently delete what you have received. Any views or opinions expressed are solely those of the author and do not necessarily represent those of Sidra Medical and Research Center. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ Disclaimer: This email and its attachments may be confidential and are intended solely for the use of the individual to whom it is addressed. If you are not the intended recipient, any reading, printing, storage, disclosure, copying or any other action taken in respect of this e-mail is prohibited and may be unlawful. If you are not the intended recipient, please notify the sender immediately by using the reply function and then permanently delete what you have received. Any views or opinions expressed are solely those of the author and do not necessarily represent those of Sidra Medical and Research Center. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] loading with Auto detect and fastqsanger options issue!
Hi, I have installed Galaxy as cluster in my local env. I have few fastq.gz files in my file system that I want to link them to galaxy instead of loading them. When I select "Auto Detect" during the loading I noticed two things. First, it is taking way longer to link the files with the AutoDetect option compared to when I chose Fastqsanger as my file type. It takes less than a second if I specify the type, i.e Fastqsanger. Any reason why is that? Is there a way to speed up the first option (Auto Detect)? Second, when it finish linking for AutoDetect option, it shows the DataType for these files as "data" rather than fastq files. Does this mean my fastq.gz files are not recognize as fastq files? To validate my fastq files, I tried to use FastqValidator tool I get an error saying "BGZF EOF marker is missing". How can I fix these files? I appreciate any kind of help, Regards, Hak Disclaimer: This email and its attachments may be confidential and are intended solely for the use of the individual to whom it is addressed. If you are not the intended recipient, any reading, printing, storage, disclosure, copying or any other action taken in respect of this e-mail is prohibited and may be unlawful. If you are not the intended recipient, please notify the sender immediately by using the reply function and then permanently delete what you have received. Any views or opinions expressed are solely those of the author and do not necessarily represent those of Sidra Medical and Research Center. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Sample Tracking Feature in Galaxy
Hi, I am trying to see if we can use Tracking Sample Features in Galaxy to collect some data from the technisians. However, I have no idea where to start. I guess I do not know how to set it up in Galaxy. Here is what I have done so far. From the admin panel, I create two forms; Sequencing Request Form, and a Sequencing Sample Form When I want to create a new Sequence Request Type it tells me that I need the two forms Creating a new request type requires two form definitions, a Sequencing Request Form, and a Sequencing Sample Form, which must be created first. Click the Create new form button to create them. However, I have already created them. The Sequence Request Form creator does not see that.How to go behind this point? Also from some online tutorials, there is a menu called Lab should show up in the main menu of Galaxy. I do not see that in mine. Is there something that I need to setup here. I appreciate your help. Regards Disclaimer: This email and its attachments may be confidential and are intended solely for the use of the individual to whom it is addressed. If you are not the intended recipient, any reading, printing, storage, disclosure, copying or any other action taken in respect of this e-mail is prohibited and may be unlawful. If you are not the intended recipient, please notify the sender immediately by using the reply function and then permanently delete what you have received. Any views or opinions expressed are solely those of the author and do not necessarily represent those of Sidra Medical and Research Center. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
