Error while local installation

[Biju]

I took the latest codebase and trying to install it in local ubuntu (13.04 64-bit) and gets the following trace. Has anyone faced similar error before ? How to work around this.

Thanks in advance.


==================================================================================================================

The following packages will be upgraded:
  libcurl3
1 upgraded, 1 newly installed, 0 to remove and 330 not upgraded.
Need to get 393 kB of archives.
After this operation, 387 kB of additional disk space will be used.
Get:1 http://us.archive.ubuntu.com/ubuntu/ raring-updates/main libcurl3 amd64 7.29.0-1ubuntu3.4 [243 kB]
Get:2 http://us.archive.ubuntu.com/ubuntu/ raring-updates/main curl amd64 7.29.0-1ubuntu3.4 [149 kB]
Fetched 393 kB in 4s (85.9 kB/s)
(Reading database ... 157592 files and directories currently installed.)
Preparing to replace libcurl3:amd64 7.29.0-1ubuntu3 (using .../libcurl3_7.29.0-1ubuntu3.4_amd64.deb) ...
Unpacking replacement libcurl3:amd64 ...
Selecting previously unselected package curl.
Unpacking curl (from .../curl_7.29.0-1ubuntu3.4_amd64.deb) ...
Processing triggers for man-db ...
Setting up libcurl3:amd64 (7.29.0-1ubuntu3.4) ...
Setting up curl (7.29.0-1ubuntu3.4) ...
Processing triggers for libc-bin ...
ldconfig deferred processing now taking place
DBG [deb.py]: _setup_apt_sources /etc/apt/sources.list.d/cloudbiolinux.list BioLinux base Edition
[localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy  bash -c "touch /etc/apt/sources.list.d/cloudbiolinux.list"
[localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy  bash -c "echo '# This file was modified for BioLinux base Edition' >> \"$(echo /etc/apt/sources.list.d/cloudbiolinux.list)\""
DBG [deb.py]: Source deb http://us.archive.ubuntu.com/ubuntu/ raring universe
DBG [deb.py]: Source deb http://us.archive.ubuntu.com/ubuntu/ raring multiverse
DBG [deb.py]: Source deb http://us.archive.ubuntu.com/ubuntu/ raring-updates universe
DBG [deb.py]: Source deb http://us.archive.ubuntu.com/ubuntu/ raring-updates multiverse
DBG [deb.py]: Source deb http://archive.canonical.com/ubuntu raring partner
DBG [deb.py]: Source deb http://downloads-distro.mongodb.org/repo/ubuntu-upstart dist 10gen
[localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy  bash -c "echo 'deb http://downloads-distro.mongodb.org/repo/ubuntu-upstart dist 10gen' >> \"$(echo /etc/apt/sources.list.d/cloudbiolinux.list)\""
DBG [deb.py]: Source deb http://cran.fhcrc.org/bin/linux/ubuntu raring/
[localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy  bash -c "echo 'deb http://cran.fhcrc.org/bin/linux/ubuntu raring/' >> \"$(echo /etc/apt/sources.list.d/cloudbiolinux.list)\""
DBG [deb.py]: Source deb http://archive.cloudera.com/debian maverick-cdh3 contrib
[localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy  bash -c "echo 'deb http://archive.cloudera.com/debian maverick-cdh3 contrib' >> \"$(echo /etc/apt/sources.list.d/cloudbiolinux.list)\""
DBG [deb.py]: Source deb http://archive.canonical.com/ubuntu raring partner
DBG [deb.py]: Source deb http://ppa.launchpad.net/freenx-team/ppa/ubuntu precise main
[localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy  bash -c "echo 'deb http://ppa.launchpad.net/freenx-team/ppa/ubuntu precise main' >> \"$(echo /etc/apt/sources.list.d/cloudbiolinux.list)\""
DBG [deb.py]: Source deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main
[localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy  bash -c "echo 'deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main' >> \"$(echo /etc/apt/sources.list.d/cloudbiolinux.list)\""
DBG [deb.py]: Source deb [arch=amd64 trusted=yes] http://research.cs.wisc.edu/htcondor/debian/stable/ squeeze contrib
[localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy  bash -c "echo 'deb [arch=amd64 trusted=yes] http://research.cs.wisc.edu/htcondor/debian/stable/ squeeze contrib' >> \"$(echo /etc/apt/sources.list.d/cloudbiolinux.list)\""
DBG [deb.py]: Source deb http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux
[localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy  bash -c "echo 'deb http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux' >> \"$(echo /etc/apt/sources.list.d/cloudbiolinux.list)\""
DBG [deb.py]: Source deb http://download.virtualbox.org/virtualbox/debian raring contrib
[localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy  bash -c "echo 'deb http://download.virtualbox.org/virtualbox/debian raring contrib' >> \"$(echo /etc/apt/sources.list.d/cloudbiolinux.list)\""
[localhost] local: echo 'export DEBIAN_FRONTEND=noninteractive' >> "$(echo ~/.bashrc)"
[localhost] local: sed -i.bak -r -e 's/^([ ]+\*\) return;;)$/#\1/g' "$(echo ~/.bashrc)"
[localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy  bash -c "echo \"postfix postfix/not_configured boolean true\" | /usr/bin/debconf-set-selections;echo \"postfix postfix/main_mailer_type select 'No configuration'\" | /usr/bin/debconf-set-selections;echo \"mysql-server-5.1 mysql-server/root_password string '(password omitted)'\" | /usr/bin/debconf-set-selections;echo \"mysql-server-5.1 mysql-server/root_password_again string '(password omitted)'\" | /usr/bin/debconf-set-selections;echo \"sun-java6-jdk shared/accepted-sun-dlj-v1-1 select true\" | /usr/bin/debconf-set-selections;echo \"sun-java6-jre shared/accepted-sun-dlj-v1-1 select true\" | /usr/bin/debconf-set-selections;echo \"sun-java6-bin shared/accepted-sun-dlj-v1-1 select true\" | /usr/bin/debconf-set-selections;echo \"grub-pc grub2/linux_cmdline string ''\" | /usr/bin/debconf-set-selections;echo \"grub-pc grub-pc/install_devices_empty boolean true\" | /usr/bin/debconf-set-selections;echo \"acroread acroread/default-viewer boolean false\" | /usr/bin/debconf-set-selections;echo \"rabbitmq-server rabbitmq-server/upgrade_previous note\" | /usr/bin/debconf-set-selections;echo \"condor condor/wantdebconf boolean false\" | /usr/bin/debconf-set-selections;echo \"ttf-mscorefonts-installer msttcorefonts/accepted-mscorefonts-eula boolean true\" | /usr/bin/debconf-set-selections;echo \"ttf-mscorefonts-installer msttcorefonts/present-mscorefonts-eula note\" | /usr/bin/debconf-set-selections;echo \"gdm shared/default-x-display-manager select gdm\" | /usr/bin/debconf-set-selections;echo \"lightdm shared/default-x-display-manager select gdm\" | /usr/bin/debconf-set-selections;echo \"postfix postfix/mailname string notusedexample.org\" | /usr/bin/debconf-set-selections;echo \"debconf debconf/priority select critical\" | /usr/bin/debconf-set-selections;"
INFO: Update GPG keys for repositories
[localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy  bash -c "wget -q -O- http://archive.cloudera.com/debian/archive.key | apt-key add -"
OK
[localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy  bash -c "wget -q -O- http://download.virtualbox.org/virtualbox/debian/oracle_vbox.asc | apt-key add -"
OK
[localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy  bash -c "apt-key adv --keyserver keyserver.ubuntu.com --recv 7F0CEB10"
Executing: gpg --ignore-time-conflict --no-options --no-default-keyring --secret-keyring /tmp/tmp.9AxQOaCwLu --trustdb-name /etc/apt//trustdb.gpg --keyring /etc/apt/trusted.gpg --primary-keyring /etc/apt/trusted.gpg --keyring /etc/apt/trusted.gpg.d//apt.postgresql.org.gpg --keyserver keyserver.ubuntu.com --recv 7F0CEB10
gpg: requesting key 7F0CEB10 from hkp server keyserver.ubuntu.com
gpg: key 7F0CEB10: public key "Richard Kreuter <richard@ >" imported
gpg: no ultimately trusted keys found
gpg: Total number processed: 1
gpg:               imported: 1  (RSA: 1)
[localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy  bash -c "apt-key adv --keyserver keyserver.ubuntu.com --recv E084DAB9"
Executing: gpg --ignore-time-conflict --no-options --no-default-keyring --secret-keyring /tmp/tmp.xFOYDlXVs7 --trustdb-name /etc/apt//trustdb.gpg --keyring /etc/apt/trusted.gpg --primary-keyring /etc/apt/trusted.gpg --keyring /etc/apt/trusted.gpg.d//apt.postgresql.org.gpg --keyserver keyserver.ubuntu.com --recv E084DAB9
gpg: requesting key E084DAB9 from hkp server keyserver.ubuntu.com
gpg: key E084DAB9: public key "Michael Rutter <marutter >" imported
gpg: Total number processed: 1
gpg:               imported: 1  (RSA: 1)
[localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy  bash -c "apt-key adv --keyserver subkeys.pgp.net --recv D018A4CE"
Executing: gpg --ignore-time-conflict --no-options --no-default-keyring --secret-keyring /tmp/tmp.d3D5bFf6o0 --trustdb-name /etc/apt//trustdb.gpg --keyring /etc/apt/trusted.gpg --primary-keyring /etc/apt/trusted.gpg --keyring /etc/apt/trusted.gpg.d//apt.postgresql.org.gpg --keyserver subkeys.pgp.net --recv D018A4CE
gpg: requesting key D018A4CE from hkp server subkeys.pgp.net
gpg: keyserver timed out
gpg: keyserver receive failed: keyserver error

Fatal error: local() encountered an error (return code 2) while executing 'sudo http_proxy=$http_proxy https_proxy=$https_proxy  bash -c "apt-key adv --keyserver subkeys.pgp.net --recv D018A4CE"'

Aborting.
master@master:~/cloudbiolinux$

[Brad Chapman]

Biju;
This looks like an intermittent connectivity error, since it was unable
to connect to the keyserver. I pushed some fixes to CloudBioLinux to
make these warnings instead of errors since it should be able to proceed
without the keys without major issues. If you update to the latest and
re-run, it should work cleanly now. Thanks much for the report,
Brad

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[Venkatesh Duvvuri]

I took the latest changes and I tried to install but I am getting the following stack trace. Can some one please help me.

DBG [fabfile.py]: Importing module cloudbio.custom.bio_nextgen
DBG [fabfile.py]: Looking for custom install function cloudbio.custom.bio_nextgen.install_velvet
INFO: Custom install for 'velvet' end time: 2014-04-01 10:00:31.226829; duration: 0:00:00.003059
INFO: Custom install for 'galaxy_webapp' start time: 2014-04-01 10:00:31.227051
DBG [fabfile.py]: Importing module cloudbio.custom.galaxy
DBG [fabfile.py]: Looking for custom install function cloudbio.custom.galaxy.install_galaxy_webapp
DBG [__init__.py]: Done setting up Galaxy/CloudMan users
[localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy  bash -c "mkdir -p '/mnt/galaxy/galaxy-app'"
[localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy  bash -c "hg clone https://bitbucket.org/galaxy/galaxy-central/ ."
warning: bitbucket.org certificate with fingerprint 67:b3:bf:9f:c5:38:0e:4c:dd:4e:8a:da:3d:11:1b:c2:a5:d1:6c:6b not verified (check hostfingerprints or web.cacerts config setting)
requesting all changes
adding changesets
adding manifests
adding file changes
added 12921 changesets with 44137 changes to 8037 files
warning: bitbucket.org certificate with fingerprint 67:b3:bf:9f:c5:38:0e:4c:dd:4e:8a:da:3d:11:1b:c2:a5:d1:6c:6b not verified (check hostfingerprints or web.cacerts config setting)
updating to branch default
3679 files updated, 0 files merged, 0 files removed, 0 files unresolved
[localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy  bash -c "chown --recursive galaxy:galaxy /mnt/galaxy/galaxy-app"
[localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy  bash -c "chown galaxy:galaxy /mnt/galaxy"
[localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy  bash -c "chown --recursive galaxy:galaxy /mnt/galaxy/galaxy-app"
[localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy su - galaxy bash -c "sed -i 's/python .\//python -ES .\//g' /mnt/galaxy/galaxy-app/run.sh"
[localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy su - galaxy bash -c "grep -q 'export DRMAA_LIBRARY_PATH=/opt/sge/lib/lx24-amd64/libdrmaa.so.1.0' /mnt/galaxy/galaxy-app/run.sh; if [ $? -eq 1 ]; then sed -i '2 a export DRMAA_LIBRARY_PATH=/opt/sge/lib/lx24-amd64/libdrmaa.so.1.0' run.sh; fi"
[localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy su - galaxy bash -c "wget --output-document=/mnt/galaxy/galaxy-app/static/images/cloud.gif http://userwww.service.emory.edu/~eafgan/content/cloud.gif"
--2014-04-01 15:37:45--  http://userwww.service.emory.edu/~eafgan/content/cloud.gif
Resolving userwww.service.emory.edu (userwww.service.emory.edu)... 170.140.53.161
Connecting to userwww.service.emory.edu (userwww.service.emory.edu)|170.140.53.161|:80... connected.
HTTP request sent, awaiting response... No data received.
Retrying.

--2014-04-01 15:38:32--  (try: 2)  http://userwww.service.emory.edu/~eafgan/content/cloud.gif
Connecting to userwww.service.emory.edu (userwww.service.emory.edu)|170.140.53.161|:80... connected.
HTTP request sent, awaiting response... No data received.
Retrying.

--2014-04-01 15:39:19--  (try: 3)  http://userwww.service.emory.edu/~eafgan/content/cloud.gif
Connecting to userwww.service.emory.edu (userwww.service.emory.edu)|170.140.53.161|:80... connected.
HTTP request sent, awaiting response... No data received.
Retrying.

--2014-04-01 15:40:07--  (try: 4)  http://userwww.service.emory.edu/~eafgan/content/cloud.gif
Connecting to userwww.service.emory.edu (userwww.service.emory.edu)|170.140.53.161|:80... connected.
HTTP request sent, awaiting response... No data received.
Retrying.

--2014-04-01 15:40:56--  (try: 5)  http://userwww.service.emory.edu/~eafgan/content/cloud.gif
Connecting to userwww.service.emory.edu (userwww.service.emory.edu)|170.140.53.161|:80... connected.
HTTP request sent, awaiting response... No data received.
Retrying.

--2014-04-01 15:41:46--  (try: 6)  http://userwww.service.emory.edu/~eafgan/content/cloud.gif
Connecting to userwww.service.emory.edu (userwww.service.emory.edu)|170.140.53.161|:80... connected.
HTTP request sent, awaiting response... No data received.
Retrying.

--2014-04-01 15:42:37--  (try: 7)  http://userwww.service.emory.edu/~eafgan/content/cloud.gif
Connecting to userwww.service.emory.edu (userwww.service.emory.edu)|170.140.53.161|:80... connected.
HTTP request sent, awaiting response... No data received.
Retrying.

--2014-04-01 15:43:29--  (try: 8)  http://userwww.service.emory.edu/~eafgan/content/cloud.gif
Connecting to userwww.service.emory.edu (userwww.service.emory.edu)|170.140.53.161|:80... connected.
HTTP request sent, awaiting response... No data received.
Retrying.

--2014-04-01 15:44:22--  (try: 9)  http://userwww.service.emory.edu/~eafgan/content/cloud.gif
Connecting to userwww.service.emory.edu (userwww.service.emory.edu)|170.140.53.161|:80... connected.
HTTP request sent, awaiting response... No data received.
Retrying.

--2014-04-01 15:45:16--  (try:10)  http://userwww.service.emory.edu/~eafgan/content/cloud.gif
Connecting to userwww.service.emory.edu (userwww.service.emory.edu)|170.140.53.161|:80... connected.
HTTP request sent, awaiting response... No data received.
Retrying.

--2014-04-01 15:46:11--  (try:11)  http://userwww.service.emory.edu/~eafgan/content/cloud.gif
Connecting to userwww.service.emory.edu (userwww.service.emory.edu)|170.140.53.161|:80... connected.
HTTP request sent, awaiting response... No data received.
Retrying.

--2014-04-01 15:47:06--  (try:12)  http://userwww.service.emory.edu/~eafgan/content/cloud.gif
Connecting to userwww.service.emory.edu (userwww.service.emory.edu)|170.140.53.161|:80... connected.
HTTP request sent, awaiting response... No data received.
Retrying.

--2014-04-01 15:48:01--  (try:13)  http://userwww.service.emory.edu/~eafgan/content/cloud.gif
Connecting to userwww.service.emory.edu (userwww.service.emory.edu)|170.140.53.161|:80... connected.
HTTP request sent, awaiting response... No data received.
Retrying.

--2014-04-01 15:48:56--  (try:14)  http://userwww.service.emory.edu/~eafgan/content/cloud.gif
Connecting to userwww.service.emory.edu (userwww.service.emory.edu)|170.140.53.161|:80... connected.
HTTP request sent, awaiting response... No data received.
Retrying.

--2014-04-01 15:49:51--  (try:15)  http://userwww.service.emory.edu/~eafgan/content/cloud.gif
Connecting to userwww.service.emory.edu (userwww.service.emory.edu)|170.140.53.161|:80... connected.
HTTP request sent, awaiting response... No data received.
Retrying.

--2014-04-01 15:50:46--  (try:16)  http://userwww.service.emory.edu/~eafgan/content/cloud.gif
Connecting to userwww.service.emory.edu (userwww.service.emory.edu)|170.140.53.161|:80... connected.
HTTP request sent, awaiting response... No data received.
Retrying.

--2014-04-01 15:51:41--  (try:17)  http://userwww.service.emory.edu/~eafgan/content/cloud.gif
Connecting to userwww.service.emory.edu (userwww.service.emory.edu)|170.140.53.161|:80... connected.
HTTP request sent, awaiting response... No data received.
Retrying.

--2014-04-01 15:52:36--  (try:18)  http://userwww.service.emory.edu/~eafgan/content/cloud.gif
Connecting to userwww.service.emory.edu (userwww.service.emory.edu)|170.140.53.161|:80... connected.
HTTP request sent, awaiting response... No data received.
Retrying.

--2014-04-01 15:53:31--  (try:19)  http://userwww.service.emory.edu/~eafgan/content/cloud.gif
Connecting to userwww.service.emory.edu (userwww.service.emory.edu)|170.140.53.161|:80... connected.
HTTP request sent, awaiting response... No data received.
Retrying.

--2014-04-01 15:54:26--  (try:20)  http://userwww.service.emory.edu/~eafgan/content/cloud.gif
Connecting to userwww.service.emory.edu (userwww.service.emory.edu)|170.140.53.161|:80... connected.
HTTP request sent, awaiting response... No data received.
Giving up.


Fatal error: local() encountered an error (return code 4) while executing 'sudo http_proxy=$http_proxy https_proxy=$https_proxy su - galaxy bash -c "wget --output-document=/mnt/galaxy/galaxy-app/static/images/cloud.gif http://userwww.service.emory.edu/~eafgan/content/cloud.gif"'

Aborting.

[Brad Chapman]

Venkatesh;
Thanks for all the patience getting this installed and for all the
reports. Apologies, we should also have disabled Galaxy setup for local
instances since this is CloudMan/AWS specific as well. I pushed fixes to
do this so we'll now avoid these installs for local
installations. Hopefully an update with the latest changes will finish
cleanly for you now,

>> an email to cloudbiolinu...@googlegroups.com <javascript:>.
>> > To post to this group, send email to cloudb...@googlegroups.com<javascript:>.