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Version number update... again...
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@dzerbino
dzerbino committed Jul 18, 2013
1 parent 0c3315a commit d799631
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Binary file modified Columbus_manual.pdf
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2 changes: 1 addition & 1 deletion Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ CATEGORIES=2
DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)

# Mac OS users: uncomment the following lines
# CFLAGS = -Wall -m64
CFLAGS = -Wall -m64

# Sparc/Solaris users: uncomment the following line
# CFLAGS = -Wall -m64
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2 changes: 1 addition & 1 deletion src/globals.h
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Expand Up @@ -38,7 +38,7 @@ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)

#define VERSION_NUMBER 1
#define RELEASE_NUMBER 2
#define UPDATE_NUMBER 9
#define UPDATE_NUMBER 10

#define MAXLINE 5000

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5 comments on commit d799631

@fgeorgatos
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Hi,

the tarball you publish as 1.2.10 does not have this update, therefor the following happens when we install it with easybuild:

fgeorgatos@gaia-59:~: $ velveth 2>&1|head
velveth - simple hashing program
Version 1.2.09

Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Compilation settings:
CATEGORIES = 2
MAXKMERLENGTH = 63

The command that installed that has been: (notice how nicely EasyBuild does the job)

fgeorgatos@gaia-59:~: $ time eb Velvet-1.2.09-ictce-5.3.0.eb --try-software-version=1.2.10 --try-amend=versionsuffix=-kmer63 --try-amend=makeopts=MAXKMERLENGTH=63

== temporary log file in case of crash /tmp/easybuild-VshLFF.log
== resolving dependencies ...
== processing EasyBuild easyconfig /tmp/Velvet-1.2.10-ictce-5.3.0-kmer63.eb
== building and installing Velvet/1.2.10-ictce-5.3.0-kmer63...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== testing...
== installing...
== taking care of extensions...
== packaging...
== postprocessing...
== sanity checking...
== cleaning up...
== creating module...
== COMPLETED: Installation ended successfully
==
WARNING: Build exited with exit code 0. 1 possible error(s) were detected in the build logs, please verify the build.

== Results of the build can be found in the log file /tmp/easybuild-Velvet-1.2.10-20131115.134556.log
== Build succeeded for 1 out of 1
== temporary log file /tmp/easybuild-VshLFF.log has been removed.

real    0m44.635s
user    0m9.237s
sys 0m1.780s


fgeorgatos@gaia-59:~: $ module av Velvet

------- /home/users/fgeorgatos/.local/easybuild/modules/all -------
Velvet/1.2.10-ictce-5.3.0-kmer63

------------------ /opt/apps/HPCBIOS/modules/bio ------------------
Velvet/1.2.07-goolf-1.4.10 Velvet/1.2.09-goolf-1.4.10
Velvet/1.2.07-ictce-5.3.0  Velvet/1.2.09-ictce-5.3.0

I suggest refreshing the tarball or, simply push out a new version, eventually.

@dzerbino
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Thanks, I updated the tarball on the EBI servers.

@fgeorgatos
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OK, but:

the file you now provide is actually a zipfile, despite having a tgz suffix; otherwise it worked:

(look for the line which has a #### WOW ####)

fgeorgatos@gaia-59:~: $ tar -ztvf /home/users/fgeorgatos/.local/easybuild/sources/v/Velvet/velvet_1.2.10.tgz
gzip: stdin has more than one entry--rest ignored
tar: Child returned status 2
tar: Error is not recoverable: exiting now
fgeorgatos@gaia-59:~: $ gunzip !$
gunzip /home/users/fgeorgatos/.local/easybuild/sources/v/Velvet/velvet_1.2.10.tgz
gzip: /home/users/fgeorgatos/.local/easybuild/sources/v/Velvet/velvet_1.2.10.tgz has more than one entry -- unchanged
fgeorgatos@gaia-59:~: $ file /home/users/fgeorgatos/.local/easybuild/sources/v/Velvet/velvet_1.2.10.tgz
/home/users/fgeorgatos/.local/easybuild/sources/v/Velvet/velvet_1.2.10.tgz: Zip archive data, at least v1.0 to extract #### WOW ####
fgeorgatos@gaia-59:~: $ mv /home/users/fgeorgatos/.local/easybuild/sources/v/Velvet/velvet_1.2.10.tgz /home/users/fgeorgatos/.local/easybuild/sources/v/Velvet/velvet_1.2.10.zip ### rename 
fgeorgatos@gaia-59:~: $ vi /tmp/Velvet-1.2.10-ictce-5.3.0-kmer63.eb ### convert .tgz to .zip
fgeorgatos@gaia-59:~: $ time eb !$ --try-amend=versionsuffix=-kmer63 --try-amend=makeopts=MAXKMERLENGTH=63 -ftime eb /tmp/Velvet-1.2.10-ictce-5.3.0-kmer63.eb --try-amend=versionsuffix=-kmer63 --try-amend=makeopts=MAXKMERLENGTH=63 -f
== temporary log file in case of crash /tmp/easybuild-q3fg19.log
== resolving dependencies ...
== processing EasyBuild easyconfig /tmp/Velvet-1.2.10-ictce-5.3.0-kmer63.eb
== building and installing Velvet/1.2.10-ictce-5.3.0-kmer63...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== testing...
== installing...
== taking care of extensions...
== packaging...
== postprocessing...
== sanity checking...
== cleaning up...
== creating module...
== COMPLETED: Installation ended successfully
==
WARNING: Build exited with exit code 0. 1 possible error(s) were detected in the build logs, please verify the build.

== Results of the build can be found in the log file /tmp/easybuild-Velvet-1.2.10-20131117.114421.log
== Build succeeded for 1 out of 1
== temporary log file /tmp/easybuild-q3fg19.log has been removed.

real    0m11.699s
user    0m9.513s
sys 0m1.392s
fgeorgatos@gaia-59:~: $ module load Velvet
fgeorgatos@gaia-59:~: $ velveth 2>&1|head
velveth - simple hashing program
Version 1.2.10

Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Compilation settings:
CATEGORIES = 2
MAXKMERLENGTH = 63
fgeorgatos@gaia-59:~: $

@dzerbino
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@dzerbino dzerbino commented on d799631 Nov 17, 2013 via email

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@fgeorgatos
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ok, now it's all fixed.

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